October 8th
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, Froberg et al. (2023) propose nanoRibo-seq, an optimised protocol which makes it possible to examine translational regulation within only a few thousand cells. Kershaw et al. (2023) offer an in-depth investigation of the global patterns seen in the mRNA interactomes of several RNA binding proteins. Lastly, Weber et al. (2023) carried out ribosome profiling in Mycoplasma pneumoniae (Mpn), a model genome-reduced bacterium. Their analysis suggests existence of yet unknown mechanisms of translational control.
Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes
Cell Reports, 2023
Froberg, J.E., Durak, O. and Macklis, J.D.
Despite the crucial role of translational control, it has been studied much less than transcriptional control in the same biological systems. This is because global transcriptional analyses, in particular RNA sequencing (RNA-seq), remain a much less challenging biochemical technique and require significantly less input material than that required to determine translational output. In this study, the authors focus on studying translation in two exemplar cortical projection neuron subtypes: callosal projection neurons (CPN) and subcerebral projection neurons (SCPN) during early postnatal development.
To reduce the required input material, the authors developed nanoRibo-seq, an optimised protocol which makes it possible to examine translational regulation within only a few thousand cells, extending the applicability of the ribosome profiling technique to a variety of cellular, tissue, and developmentally dynamic systems. While translation efficiency for the majority of genes is highly correlated between subtypes, nanoRibo-seq was used to identify translational differences between CPN and SCPN and they found that several dozen genes exhibit differential translation, suggesting multi-level regulation of gene output between subtypes. Additionally, both CPN and SCPN were found to actively translate short upstream open reading frames (uORFs), specifically in mRNAs of genes involved in synapse organisation and axon development. Translation of uORFs in these mRNAs was found to inhibit translation of their main coding sequence.
Translation factor and RNA binding protein mRNA interactomes support broader RNA regulons for post-transcriptional control
Journal of Biological Chemistry, 2023
Kershaw, C.J., Nelson, M.G., Castelli, L.M., Jennings, M.D., Lui, J., Talavera, D., Grant, C.M., Pavitt, G.D., Hubbard, S.J. and Ashe, M.P.
It is widely believed that the poly(A) tail at the mRNA 3’ end and 5′ cap modifications play important roles in translation and shield mRNAs from degradation through interaction with certain translation initiation factors. Additionally, by promoting or suppressing the recruitment of mRNAs to the translation machinery, a variety of RNA binding proteins (RBPs) can affect the fate of an mRNA. However, it remains unclear how an individual mRNA is selected for translation from the complex pool of transcripts. The authors have previously reported the varied interactions between individual mRNAs and translation initiation factors, but have not addressed mRNA degradation and storage, or translation initiation factors that interact with the small ribosomal subunit and participate in processes like scanning and start codon recognition.
They generated additional interaction profiles from RNA immunoprecipitations of translation initiation factors such as the γ subunit of eIF2, and the b subunit of eIF3, as well as Lsm1 and Pat1, two RBPs involved in the storage and degradation of mRNA. They also redefine and expand their mRNA groupings based on the integrated interaction properties of the generated profiles. These analyses pinpoint specific groups of mRNAs with comparable control, which likely form the basis for the creation of proteins with related cellular functions.
Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium
Molecular Systems Biology, 2023
Weber, M., Sogues, A., Yus, E., Burgos, R., Gallo, C., Martínez, S., Lluch‐Senar, M. and Serrano, L.
Understanding the mechanisms of translation control has been made possible in large part by the ribosome profiling technique. Using mathematical models, analysis of ribosome profiling data has revealed factors that influence local variation in ribosome density and translation elongation rates. However, the initiation and elongation rates of a gene cannot be predicted only by ribosome density, as a rise in initiation rate or a fall in average elongation rate along the transcript can cause a global increase in ribosome density. To assess translation efficiency, further measurements of protein synthesis, turnover, and abundance are therefore required. In this study, the authors carried out ribosome profiling in Mycoplasma pneumoniae (Mpn), a model genome-reduced bacterium.
They evaluated absolute protein abundances for 75% of the genes (528 proteins) using a quantitative mass spectrometry method, and calculated the initiation and elongation rates for 475 genes, 73 with high precision, by combining the absolute quantifications of mRNA abundances, protein abundances, and protein half-lives with ribosome density. Despite over 160-fold variation in gene initiation rates, the majority of the known parameters had little impact on translation efficiency in Mpn. Their findings point to a general pattern of elongation rate adaptation to initiation rate so as to maintain roughly constant ribosome density. Although there were over 100-fold changes in tRNA abundances, these variations did not fully account for codon elongation rates. Additionally, they report that local elongation velocities are slowed down by internal Shine Dalgarno-like patterns. The combination of all known factors and parameters was insufficient to explain observed translation patterns suggesting existence of yet unknown mechanisms for translational control.