Poster abstracts
Poster number 87 submitted by Vincent Lawal
Caulobacter RppH and NudC have Direct and Indirect Effects on mRNAs
Vincent A. Lawal (Departments of Biological Sciences and Chemistry, Wayne State University, Detroit, MI), Imalka W. Ratyhnayaka-Mudiyanselage (Departments of Biological Sciences and Chemistry, Wayne State University, Detroit, MI), Hadi Yassine (Departments of Biological Sciences and Chemistry, Wayne State University, Detroit, MI), Vidhyadhar Nandana (Departments of Biological Sciences and Chemistry, Wayne State University, Detroit, MI), Jeremy G. Bird (Departments of Chemistry and Biological Sciences, Wayne State University, Detroit, MI), Jared M. Schrader (Departments of Biological Sciences and Chemistry, Wayne State University, Detroit, MI)
Abstract:
In eukaryotic cells, the 5’ m7G “cap” protects cellular mRNAs from degradation and promotes their translation. In bacteria, 5’ PPP or 5’ NAD/H “cap”-like modifications have been shown to protect mRNAs from degradation (Deana et al., 2008; Bird et al., 2016), yet their global roles in mRNA decay are poorly understood. To investigate the roles of 5’ PPP or 5’ NAD/H modifications on bacterial mRNA metabolism, we deleted the 5’ PPP decapping enzyme (rppH) or 5’ NAD/H decapping enzyme (nudC) from the Caulobacter crescentus genome and performed rif-seq experiments to measure mRNA lifetimes. We found only a small subset of mRNAs were stabilized in either of the decapping mutant strains, suggesting that these 5’ modifications have little impact on the decay of modified mRNAs in bacteria. To investigate other functions of the 5’ modifications, we investigated whether decapping mutants impact the formation of BR-bodies, which are biomolecular condensates known to organize mRNA decay machinery (Muthunayake et al., 2020). We observed that decapping enzyme deletions significantly reduce BR-bodies, suggesting that decapped RNA may promote BR-body phase separation. Finally, we observed that decapping mutants show no phenotype in the exponential growth of C. crescentus cells and discovered that they are more strongly expressed in the stationary phase, where we see they lead to significant defects in growth out of the stationary phase. Overall, this suggests that 5’ RNA “cap” modifications in bacteria have more specialized functions compared to the well-established roles in eukaryotes.
References:
Deana, A., Celesnik, H., & Belasco, J.G. (2008). The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature, 451(7176), 355-358. https://doi.org/10.1038/nature06475.
Bird, J.G., Zhang, Y., Tian, Y., Panova, N., Barvík, I., Greene, L., Liu, M., Buckley, B., Krásný, L., Lee, J.K., Kaplan, C.D., Ebright, R.H., Nickels, B.E. (2016). The mechanism of RNA 5′ capping with NAD+, NADH, and desphospho-CoA. Nature, 535(7612), 444–447. https://doi.org/10.1038/nature18622.
Muthunayake, N.S., Tomares, D.T., Childers, W.S., & Schrader, J.M. (2020). Phase-separated bacterial ribonucleoprotein bodies organize mRNA decay. Wiley Interdisciplinary Reviews: RNA, 11(6), e1599. https://doi.org/10.1002/wrna.1599.
Keywords: Decapping enzymes, BR-bodies, RNA decay, Rifampicin-sequencing