The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions

Nandana, Vidhyadhar; Rathnayaka-Mudiyanselage, Imalka W.; Muthunayake, Nisansala S.; Hatami, Ali; Mousseau, C. Bruce; Ortiz-Rodríguez, Luis A.; Vaishnav, Jamuna; Collins, Michael; Gega, Alisa; Mallikaarachchi, Kaveendya S.; Yassine, Hadi; Ghosh, Aishwarya; Biteen, Julie S.; Zhu, Yingxi; Champion, Matthew M.; Childers, W. Seth; Schrader, Jared M.

doi:10.1016/j.celrep.2023.113229

Cited by 8 publications

(4 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This suggests that RNase E’s phase-separation with its 5’ UTR promotes more rapid RNA cleavage, perhaps by increasing the local concentration of RNA and RNase E within the condensate and may also explain why RNase E IDR deletion mutants have been found to globally slow mRNA decay (13, 22). We also observed previously that RNase E condensates are observable within seconds after the addition of RNA, suggesting that phase separation of BR-bodies is also a rapid process (20). Importantly, the RNA degradosome binding partner PNPase, which is a 3’ to 5’ exoribonuclease, was also shown to have increased exonucleolytic activity in the presence of RNase E droplets (23).…”

Section: Discussionsupporting

confidence: 82%

“…We also observed that deletion of the N-terminal S1 domain, which binds RNA, or deletion of the catalytic E/G domain also abolished autoregulation (Fig S3C), suggesting a fully functional N-terminal domain is required for autoregulation. The IDR was found to be necessary and sufficient to form BR-bodies(13, 20), which allows RNase E to phase-separate with RNA and stimulates RNA decay activity in vivo (7, 13). To test whether the IDR promotes 5’ UTR cleavage in vitro , we purified full length RNase E and RNase E lacking the IDR.…”

Section: Resultsmentioning

confidence: 99%

“…Biomolecular condensation therefore provides a general organizational strategy for bacteria to organize their biochemical pathways in the absence of membrane-bound organelles. Indeed, many bacterial enzymes from various multi-step biochemical pathways have been found to phase-separate and form biomolecular condensates (20,(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41) suggesting that this strategy of subcellular organization may be utilized to organize a variety of other biochemical pathways in bacteria.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Caulobacter crescentusRNase E condensation contributes to autoregulation and fitness

Nandana,

Al-Husini,

Vaishnav

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

RNase E is the most common RNA decay nuclease in bacteria, setting the global mRNA decay rate and scaffolding formation of the RNA degradosome complex and BR-bodies. To properly set the global mRNA decay rate, RNase E fromEscherichia coliand neighboring γ-proteobacteria were found to autoregulate RNase E levels via the decay of its mRNA’s 5’ UTR. While the 5’ UTR is absent from other groups of bacteria in the Rfam database, we identified that the α-proteobacteriumCaulobacter crescentusRNase E contains a similar 5’ UTR structure that promotes RNase E autoregulation. In both bacteria, the C-terminal IDR of RNase E is required for proper autoregulation to occur, and this IDR is also necessary and sufficient for RNase E to phase-separate, generating BR-bodies. Usingin vitropurified RNase E, we find that the IDR’s ability to promote phase-separation correlates with enhanced 5’ UTR cleavage, suggesting that phase-separation of RNase E with the 5’ UTR enhances autoregulation. Finally, using growth competition experiments we find that a strain capable of autoregulation rapidly outcompetes a strain with a 5’ UTR mutation that cannot autoregulate, suggesting autoregulation promotes optimal cellular fitness.

show abstract

Section: Discussionsupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Caulobacter crescentusRNase E condensation contributes to autoregulation and fitness

Nandana,

Al-Husini,

Vaishnav

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Notably, our discovery that ribonucleases responsible for mRNA degradation are excluded from stress granules contrasts with findings in C. crescentus , where the ribonuclease RNaseE is integral to the formation of BR bodies 19 . Instead, the organization of BR bodies appears to modulate degradosome activity 20, 21 . Furthermore, these findings hold promise for informing future strategies aimed at developing tailored synthetic aggresomes for therapeutic applications involving mRNA, such as vaccines and gene silencing.…”

Section: Discussionmentioning

confidence: 99%

Bacterial stress granule protects mRNA through ribonucleases exclusion

Pei,

Xian,

Yan

et al. 2024

Preprint

View full text Add to dashboard Cite

Membraneless droplets formed through liquid-liquid phase separation (LLPS) play a crucial role in mRNA storage, enabling organisms to swiftly respond to environmental changes. However, the mechanisms underlying mRNA integration and protection within droplets remain unclear. Here, we unravel the role of bacterial aggresomes as stress granules (SGs) in safeguarding mRNA during stress. We discovered that upon stress onset, mobile mRNA molecules selectively incorporate into individual proteinaceous SGs based on length-dependent enthalpic gain over entropic loss. As stress prolongs, SGs undergo compaction facilitated by stronger non-specific RNA-protein interactions, thereby promoting recruitment of shorter RNA chains. Remarkably, mRNA ribonucleases are repelled from bacterial SGs, due to the influence of protein surface charge. This exclusion mechanism ensures the integrity and preservation of mRNA within SGs during stress conditions, explaining how mRNA can be stored and protected from degradation. Following stress removal, SGs facilitate mRNA translation, thereby enhancing cell fitness in changing environments. These droplets maintain mRNA physiological activity during storage, making them an intriguing new candidate for mRNA therapeutics manufacturing.

show abstract

Proteomic composition of eukaryotic and bacterial RNA decay condensates suggests convergent evolution

Rathnayaka-Mudiyanselage,

Nandana,

Schrader

2024

Current Opinion in Microbiology

View full text Add to dashboard Cite

The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions

Cited by 8 publications

References 72 publications

Caulobacter crescentusRNase E condensation contributes to autoregulation and fitness

Caulobacter crescentusRNase E condensation contributes to autoregulation and fitness

Bacterial stress granule protects mRNA through ribonucleases exclusion

Proteomic composition of eukaryotic and bacterial RNA decay condensates suggests convergent evolution

Contact Info

Product

Resources

About