April 21st, 2024
Recent Publications Harnessing the Power of Translatomics.
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, Dos Santos et al. delve into the regulation of the ribosome quality control complex, Shields et al. shed light on bacterial rRNA methylation, and Huang et al. introduce NanoSPA, a Nanopore pipeline for simultaneous analysis of specific posttranscriptional mRNA modifications.
Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells
Scientific Reports, 2024
Otávio Augusto Leitão Dos Santos, Rodolfo L. Carneiro, Rodrigo D. Requião, Marcelo Ribeiro-Alves, Tatiana Domitrovic & Fernando L. Palhano
This research delves into the intricate mechanisms of the ribosome quality control (RQC) complex and its implications on cellular function and transcriptional regulation. Using published transcriptomics and translatomics datasets, the authors investigate how disruptions in RQC components affect cell growth and transcriptome profiles. Haploinsufficiency analysis reveals that deficiencies in one allele of RQC genes do not significantly alter the wild-type phenotype, suggesting cellular tolerance to translational perturbations caused by RQC impairment. Transcriptional responses to RQC disruption, particularly in genes regulated by LTN1 and NEMF, highlight pathways involved in ubiquitination processes and ribosome assembly. Surprisingly, knockdown experiments show that certain genes with similar transcriptional responses to RQC disruptions are not directly involved in co-translational quality control pathways.
Furthermore, analysis of mRNA expression levels in human tissues across different age ranges suggests age-dependent downregulation of RQC components, particularly NEMF and LTN1, potentially impacting proteostasis and contributing to neurodegenerative diseases. TCF25, another essential RQC component, exhibits distinct regulation patterns and functions beyond co-translational control, further emphasizing the complexity of RQC-mediated processes. Post-translational regulation of TCF25, possibly through ubiquitination, underscores the intricate regulatory networks governing RQC activity. Overall, the study sheds light on the fundamental role of the RQC complex in maintaining cellular homeostasis and highlights its relevance in age-related proteostasis dysregulation and neurodegenerative diseases.
Epitranscriptional m6A modification of rRNA negatively impacts translation and host colonization in Staphylococcus aureus
PLOS Pathogens, 2024
Kathryn E. Shields, David Ranava, Yongjun Tan, Dapeng Zhang, Mee-Ngan F. Yap
This article explores the significance of adenosine methylation in RNA, particularly focusing on its implications for bacterial physiology and antibiotic resistance. Adenosine methylation, specifically at the A2058 nucleotide in bacterial ribosomal RNA (rRNA), has been associated with antibiotic resistance, particularly to macrolides, lincosamides, and streptogramin B. The methylation alters the ribosomal structure, reducing the affinity for these antibiotics and allowing bacteria to evade the immune response, facilitating infections.
The study delves into the mechanisms underlying the regulation of methyltransferase genes and their impact on antibiotic resistance. It highlights the role of erm genes, particularly in conferring resistance to MLS antibiotics, and their prevalence among nosocomial bacteria. The research elucidates how mutations affecting translation initiation or mRNA stability contribute to erm gene upregulation, thereby promoting antibiotic resistance.
Furthermore, the article investigates the physiological consequences of adenosine methylation on bacterial fitness and virulence. Using methicillin-resistant Staphylococcus aureus (MRSA) as a model, it was demonstrated that constitutive methylation of ribosomes leads to reduced translational efficiency and altered gene expression, particularly affecting virulence factors. The research also employs genome-wide ribosome profiling to elucidate the global impact of ribosomal methylation on translation. It reveals altered mRNA levels and decoding of virulence-associated genes, shedding light on the mechanisms underlying the fitness loss observed in methylated ribosomes.
Overall, these findings underscore the significance of adenosine methylation in bacterial physiology, antibiotic resistance, and pathogenesis. It provides valuable insights into the molecular mechanisms governing ribosomal methylation and its consequences, offering potential avenues for combating antibiotic resistance in bacterial infections.
Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination
Nature Biotechnology, 2024
The article discusses the significance of two prevalent modifications found in mammalian messenger RNA (mRNA), namely N6-methyladenosine (m6A) and pseudouridine (Ψ). While m6A has been extensively studied and is known to influence various cellular processes including mRNA stability, splicing, and translation, Ψ’s primary function – exemplified by COVID-19 mRNA vaccines – is to aid innate immune avoidance. However, understanding the interplay between these modifications within the same mRNA transcript remains a gap in research.
To address this, the authors developed a novel nanopore sequencing pipeline called NanoSPA, capable of simultaneously analyzing m6A and Ψ modifications. They applied this pipeline to human transcriptomes and polysome profiling data, revealing insights into the co-dependence and antagonism between these modifications. NanoSPA utilizes a fused workflow for base calling, alignment, and feature extraction, enabling efficient processing and storage.
The study revealed that transcripts with more Ψ tend to have fewer m6A sites, and vice versa, suggesting a mutual exclusion phenomenon. Furthermore, knockdown experiments of key writers for m6A and Ψ provided insights into their regulatory roles. METTL3 knockdown reduced m6A levels universally, while TRUB1 knockdown decreased Ψ levels, leading to alterations in translation efficiency. Polysome profiling indicated a synergistic effect of m6A and Ψ on translation, with Ψ exerting a larger influence. Overall, the study underscores the importance of simultaneous investigation of mRNA modifications and reveals intricate dynamics governing mRNA regulation and translation efficiency, with implications for understanding disease mechanisms and therapeutic development.