
June 11th
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 Duviau et al. explore the RNA degradosome in E.coli, Hadjeras et al. looks at the small proteome in the plant symbiont Sinorhizobium meliloti and Ma et al. look at lipid metabolism in Acer truncatum.
When translation elongation is impaired, the mRNA is uniformly destabilized by the RNA degradosome, while the concentration of mRNA is altered along the molecule
Nucleic Acids Research, 2023
Duviau, M.P., Chen, F., Emile, A., Cocaign-Bousquet, M., Girbal, L. and Nouaille, S.
Understanding the interplay of transcription, translation, and mRNA degradation in Escherichia coli remains a challenge, particularly regarding the impact of translation on mRNA degradation and transcription.
To investigate this relationship, researchers manipulated translation initiation and elongation, observing effects on mRNA stability and concentration. Decreasing translation initiation efficiency resulted in reduced stability and concentration of lacZ mRNAs, as well as decreased ribosome loading, leading to reduced synthesis of β-galactosidase protein. This reduced stability effects was uniform throughout the mRNA molecule, and there was no accumulation of degradation intermediates.
Polysome profiling showed that most mRNAs were actively being translated, with only a small fraction being ribosome-free. The presence of an untranslated portion destabilized the mRNA, regardless of its length. Premature termination of translation led to a decrease in local mRNA concentrations downstream of the stop codon. To confirm this, restoring translation at the internal stop codon prevented the decrease in mRNA concentrations downstream of the stop codon, confirming the impact of uncoupling between translation and transcription. The study also finds that is destabiling of RNA depends on RNase E activity.
This study reveals a strong connection between mRNA degradation and its translation status. When ribosome density is low or there is a region without ribosomes, the entire mRNA molecule becomes destabilized. This destabilization results in a decrease in overall concentration, while transcriptional changes lead to localized concentration variations along the mRNA molecule. The interplay between transcription, translation, and mRNA degradation governs quality control and mRNA concentrations, forming a coordinated mechanism that shapes gene expression in bacteria.
Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics
microLife, 2023
Hadjeras, L., Heiniger, B., Maaß, S., Scheuer, R., Gelhausen, R., Azarderakhsh, S., Barth-Weber, S., Backofen, R., Becher, D., Ahrens, C.H. and Sharma, C.M.
Despite the abundance of available data, there is a lack of knowledge about small open reading frame (sORF)-encoded proteins (SEPs), which are proteins consisting of less than 50 or 100 amino acids (aa). However, there is a growing interest in studying small proteomes due to emerging evidence highlighting the crucial roles played by small proteins in various physiological functions.
In this study, the researchers developed and applied a Ribo-seq workflow to map the translatome of S. meliloti 2011 under free-living conditions in a minimal medium. They successfully optimized the Ribo-seq protocol for S. meliloti, using RNase I digestion to generate ribosome footprints and obtain high-quality ribo-seq data. By combining this ribo-seq technique with mass spectrometry, and Western blot analysis of C-terminally tagged proteins, they identified 48 previously unknown small proteins (SEPs) with a length below 70 amino acids, expanding the annotation of SEPs in S. meliloti by approximately 15% compared to previous annotations.
These novel sORFs were typically shorter in length and often located in non-coding RNAs, antisense RNAs, or untranslated regions. Notably, this study provides valuable insights into the translatome of S. meliloti and represents the first Ribo-seq analysis of a member of the Hyphomicrobiales group.
Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum
BMC Biology, 2023
Ma, Q., Wang, Y., Li, S., Wen, J., Zhu, L., Yan, K., Du, Y., Li, S., Yan, L., Xie, Z. and Lyu, Y.
Post-transcriptional regulation plays a significant role in influencing the production of enzymes responsible for lipid biosynthesis reactions. However, limited information is currently available concerning the post-transcriptional control of lipid biosynthesis specifically in A. truncatum – a versatile oil-producing woody tree.
Based on a previous study by the authors, a significant increase in the oil proportion of A. truncatum seeds from 85 to 115 days after flowering (DAF) was revealed. To understand the genetic regulation of seed development during this period, ribosomal profiles were analyzed using Ribo-seq, RNA-seq, and proteomic data from seeds collected at 85 and 115 DAF. Differential expression analysis at multiple levels identified key genes that underwent significant changes between the two time points.
The authors extensively characterized key genes involved in biosynthesis (LACS, FAD2, FAD3, and KCS) and identified regulators (MYB, ABI, bZIP, and Dof) that influence lipid biosynthesis through post-translational regulations. The analysis of translational features revealed that genes with translated upstream open reading frames (uORFs) tended to have lower translation efficiency compared to genes without translated uORFs.
Furthermore, the study found that seeds collected at 115 DAF contained higher levels of oleic acid, linoleic acid, and nervonic acid compared to seeds collected at 85 DAF. These disparities at the transcriptional, translational, and protein levels demonstrated the reproducibility and clear distinctions between the two time points.