Poster abstracts

Poster number 116 submitted by Imalka W Rathnayaka-Mudiyanselage

Interplay between 5’ nucleotide modifications and BR-body formation in bacterial mRNA decay

Imalka W. Rathnayaka-Mudiyanselage (Department of Chemistry, Department of Biological Sciences, Wayne State University Current affiliation Department of Human Genetics, University of Michigan), Jeremy Bird (Department of Biological Sciences, University of Delaware), Vidhyadhar Nandana (Department of Biological Sciences, Wayne State University), Jared M. Schrader (Department of Biological Sciences, Wayne State University)

Abstract:
The chemical structure of the 5’ nucleotide of mRNA is a key factor of governing RNA decay in both eukaryotes and bacteria. Eukaryotic mRNAs are protected from the 5’-end dependent degradation by a 5’ 7-methylguanylate (m7G) cap, and its enzymatic removal leaves a 5’-end monophosphate (5’P) that induces a rapid degradation of the mRNA. In contrast, bacterial mRNAs were long assumed to only contain a 5'-end triphosphate (5’PPP) and, recent evidence shows that some bacterial RNA species bear a 5'-end nicotinamide adenine dinucleotide (NAD), both of which can protect RNAs from decay. In bacteria, conversion of the 5’PPP or NAD caps to 5’P are catalyzed by the decapping enzymes, RppH and NudC. Previous studies have been limited in the number of modified mRNAs tested, and it is currently unknown how these 5’-end modifications function across the bacterial transcriptome. The steps of 5’-end “decapping” which initiate mRNA decay in eukaryotes are thought to occur in ribonucleoprotein (RNP) granules such as P-bodies that contain the decapping enzymes. Bacteria also form similar RNP granules, termed bacterial ribonucleoprotein bodies (BR-bodies) which share functional similarities with eukaryotic RNP granules, however, the presence of decapping enzymes is unknown. Therefore, we want to understand the coordination of 5’ decapping enzymes with BR-bodies and how the 5’-end modification state impacts mRNA decay in bacteria. In our preliminary experiments, by generating the deletion strains of rppH and nudC from C. crescentus, we found that their activity promotes robust BR-body formation. RNA-seq experiment was performed to measure the global mRNA decay rates in deletion strains and mRNA decay rates in rppH deletion strain suggest that RppH likely “decaps” only a subset of mRNAs. Gene Ontology term enrichment found those RppH target mRNAs coding proteins mainly involved in gene amino acid metabolism. Current progress to analyze global mRNA decay rates in nudC deletion strains will also be presented. Ultimately, the findings of our study will provide a valuable resource to gain important insights into how nudix hydrolases modify bacterial mRNAs, leading to impacts on BR-body formation and mRNA decay in bacteria.

References:
Nandana, V. and Rathnayaka-Mudiyanselage, I.W., et al. “The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions.” bioRxiv (2023): 524314. (Accepted in Cell Reports)
Al-Husini, N., et al. "α-Proteobacterial RNA Degradosomes Assemble Liquid-Liquid Phase-Separated RNP Bodies." Molecular cell 71.6 (2018): 1027-1039.
Luciano, D. J., et al. “A novel rna phosphorylation state enables 5′ end-dependent degradation in escherichia coli.” Molecular Cell 67.1 (2017): 44-54.
Banani, S. F., et al. “Biomolecular condensates: organizers of cellular biochemistry, Nature reviews.” Molecular cell biology 18 (2017): 285-298.

Keywords: Decapping enzymes, BR-bodies, mRNA modifications