March 31st, 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, we delve into the intricacies of genetic decoding in plants and humans. Discoveries include the role of lncRNAs in stem cell differentiation, the unprecedented plasticity of stop codons in plant genetics, and the impact of the BnVIT-L2 gene on plant growth under iron stress, offering new insights into biology and agriculture.
Unveiling Polysomal Long Non-Coding RNA Expression on the First Day of Adipogenesis and Osteogenesis in Human Adipose-Derived Stem Cells
International Journal of Molecular Science, 2024
Bonilauri, B., Ribeiro, A.L., Spangenberg, L. and Dallagiovanna, B.
This paper investigates the roles of long non-coding RNAs (lncRNAs) in signalling the transformation of human adipose-derived stem cells (hASCs) into fat (adipocytes) and bone cells (osteocytes). It aims to unravel the complex molecular mechanisms steering stem cell differentiation, shedding light on the potential implications for addressing obesity, metabolic syndromes, and bone-related conditions.
Using polysome profiling, the authors identify 90 uniquely ribosome-regulated lncRNAs during these differentiation stages, with a particular focus on certain lncRNAs, such as LINC02202 and LINC01119. These molecules are shown to influence key pathways and gene regulation processes involved in adipogenesis and osteogenesis. Interactions between lncRNAs and microRNAs, among other factors, play a pivotal role in determining the fate of cells, guiding them through their differentiation journeys. For instance, the study notes that LINC02202 significantly impacts adipogenesis through the PI3K signaling pathway and shows distinct expression at early differentiation stages.
Additionally, the paper brings to light the identification of small open reading frames (smORFs) within lncRNAs, which are capable of encoding microproteins. These microproteins are implicated in the differentiation processes and overall metabolic activities of the cells. This groundbreaking finding paves the way for new lines of inquiry into stem cell behavior and offers fresh perspectives for the development of treatments targeting metabolic disorders and skeletal diseases.
Readthrough events in plants reveal plasticity of stop codons
Cell Reports, 2024
Zhang, Y., Li, H., Shen, Y., Wang, S., Tian, L., Yin, H., Shi, J., Xing, A., Zhang, J., Ali, U. and Sami, A.
This research highlights the significant biological implications of stop-codon readthrough (SCR), a phenomenon that remains largely unexplored in plant biology. Unlike non-SCR transcripts, plant SCR candidates typically feature shorter transcript lengths with fewer exons and splice variants, indicating a potential strategy for enhancing gene functionality and environmental adaptability.
Utilizing high-resolution mass spectrometry, the researchers revealed that stop codons implicated in SCR events can be recoded to any of the 20 standard amino acids, a flexibility not previously documented. This recoding-potential challenges traditional understandings of genetic decoding and is partly explained by the presence of suppressor tRNA and near-cognate tRNAs, although not all recoding instances align with current models, suggesting areas for further investigation.
The authors also employed ribosome profiling (Ribo-seq) by analysing datasets from 56 maize samples. These analyses shed light on how SCR events preferentially occur near telomeres and identify unique non-conserved extensions in protein sequences, implying a selection for protein-coding functions. These extensions, observed in the structural and subcellular localizations of proteins, suggest significant roles in plant biology. Notably, the basic transcription factor 3 in maize exhibits considerable changes due to SCR, underlining the functional implications of these extensions.
These findings offer valuable insights into the genetic decoding flexibility, expanding the current understanding of the plant proteome and laying groundwork for future research in plant genetics and protein functionality.
Over-expression of the BnVIT-L2 gene improves the lateral root development and biofortification under iron stress
Plant Physiology and Biochemistry, 2024
The vacuolar iron transporter (VIT) family plays a key role in the uptake and sequestration of iron ions within vacuoles. In this research, the BnVIT-L2 gene from Brassica napus was successfully cloned for the first time, revealing its expression across various tissues and organs, triggered by iron stress. The BnVIT-L2 protein, situated in the vacuolar membranes, contributes to maintaining iron homeostasis by binding to iron and other bivalent metal ions.
The investigators explored the consequences of BnVIT-L2 overexpression by creating transgenic Arabidopsis (BnVIT-L2/At) and Brassica napus (BnVIT-L2-OE) plants. These modified plants demonstrated improved growth parameters, such as enhanced root development and increased chlorophyll and iron levels under iron-deficient conditions, underscoring the gene’s crucial role in counteracting iron stress.
To gain deeper insight into the underlying molecular mechanisms, the study employed Ribosome profiling (Ribo-seq) to compare gene expression variations between BnVIT-L2-OE and control K407 plants under iron stress. This analysis unveiled significant changes in 12,651 genes, with a particular emphasis on the activation of antioxidant pathways, suggesting BnVIT-L2’s integral role in combating oxidative stress caused by iron deficiency.
In conclusion, the research highlights the significant function of the BnVIT-L2 gene in regulating iron assimilation and stress response, underscored by detailed translatomic insights into reactive oxygen species (ROS) management. The findings lay a solid foundation for future investigations into enhancing plant growth and developing biofortification strategies in environments deficient in iron, providing promising directions for advancements in agricultural practices.