Aug 2026· Cell Reports· Vol 45 9, pp.
117887
· 0 citations· 88 references
Medicine
TL;DR
It is proposed that MraW modification of 16S rRNA enhances translation efficiency in general, and that specific transcripts have evolved structural features that fine-tune protein levels that may be prevalent in bacteria which exhibit uncoupled transcription and translation.
Abstract
Bacterial ribosomal RNAs (rRNAs) are decorated with conserved nucleotide modifications, but the functionality of these modifications is often underexplored. MraW (RsmH) is a 16S rRNA methyltransferase. Here, we report that deletion of mraW corrects a late-stage sporulation defect in Bacillus subtilis by bypassing a sporulation checkpoint. Ribosomes purified from ΔmraW cells display a ∼2-fold decrease in translation efficiency; in vivo, ΔmraW cells produced decreased levels of the sporulation checkpoint protein CmpA. Reduced production of CmpA is mediated by mRNA sequences that form a stem-loop which occludes early cmpA codons. Proteomic analysis revealed that MraW mediates production of multiple proteins, some of whose mRNA form similar structures as the cmpA transcript. We propose that MraW modification of 16S rRNA enhances translation efficiency in general, and that specific transcripts have evolved structural features that fine-tune protein levels. This type of control may be prevalent in bacteria which exhibit uncoupled transcription and translation.
Trans-translation and bL27 data are linked and support a model in which the amino terminus of bL27 acts as a gatekeeper to prevent tmRNA from sterically interfering with tRNA (transfer RNA) on the ribosome.
Divyasorubini Seerpatham, George Wanes, Chathuri Pathirage et al.· Science Advances· 0 citations
This work structurally characterize chimeric ribosomes derived from Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae using cryo-electron microscopy and uncover a potential relationship between 16S ribosomal RNA (rRNA) stability and translation efficiency, providing new insights into rRNA structural malleability.
Tushar Raskar, Alan Costello, A. Badran et al.· Nucleic Acids Research· 0 citations
By integrating rRNA and snoRNA sequencing approaches, this work has built a comprehensive profile of rRNA modification dynamics during early embryonic cell fate decisions, highlighting potential regulatory mechanisms for ribosome heterogeneity during development.
Tessa W. Y. Chan, Ivana Barbaric, Emma E. Thomson· bioRxiv· 0 citations
A quantitative live-cell imaging framework is developed that resolves distinct kinetic phases of SG assembly at single-cell resolution and combines these measurements with single-cell analysis of protein synthesis and identifies the conserved eIF4B RRM as a regulator of productive higher-order organization of the translation initiation machinery.
Jessica Bolivar, N. DeCuzzi, Elijah Kofke et al.· bioRxiv· 0 citations
Accurate termination of protein synthesis is paramount for the integrity of the cellular proteome, yet the dynamics and fidelity of ribosome termination remain poorly understood. Here, we establish a profiling strategy to capture terminating ribosomes in mammalian cells and reveal a substantial heterogeneity in ribosome pausing at individual stop codons. We identify a sequence motif upstream of the stop codon that promotes termination pausing, a finding supported by massively parallel reporter assays. Unexpectedly, reduced termination pausing increases the likelihood of stop codon slippage, giving rise to proteins with heterogeneous C-terminal extensions. Mechanistically, we show that sequence-dependent termination pausing is consistent with post-decoding mRNA scanning by the 3′ end of 18 S rRNA. We further uncover tissue-specific patterns of termination pausing that correlate with the stoichiometry of Rps26, which potentially modulates mRNA:rRNA interactions. Together, these results suggest termination pausing as a distinct translational signature shaped by mRNA sequence contexts, ribosome heterogeneity, and cell type-specific translational control.
Accurate termination of protein synthesis is paramount for the integrity of cellular proteome, yet the dynamics and fidelity of ribosome termination remain poorly understood. Here, we establish a profiling strategy to capture terminating ribosomes in mammalian cells and reveal a substantial heterogeneity in ribosome pausing at individual stop codons. We identify a sequence motif upstream of the stop codon that promotes termination pausing, a finding validated by massively paralleled reporter assays. Unexpectedly, reduced termination pausing increases the likelihood of stop codon slippage, giving rise to proteins with heterogenous C-terminal extensions. Mechanistically, we show that sequence-dependent termination pausing arises from post-decoding mRNA scanning by the 3’ end of 18S rRNA. We further uncover tissue-specific patterns of termination pausing that correlates with the stoichiometry of Rps26, which modulates mRNA:rRNA interactions. Together, these results establish termination pausing as a distinct translational signature shaped by mRNA sequence contexts, ribosome heterogeneity, and cell type-specific translational control.
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
