July 16th
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, Jiang et al. (2023) characterized PRRC2B in translational regulation using human embryonic kidney (HEK293T) cells. Kito Y et al. (2023) identified components of eIF4A-bound scanning ribosomes and determined the function of ASCC in the regulation of translation initiation. Lastly, Montañés et al. (2023) provided valuable insights into gene duplication and de novo gene birth both contributing to new gene formation by comparing properties in yeasts and flies.
RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression
Nucleic Acids Research, 2023
Jiang, F., Hedaya, O., Khor, E., Wu, J., Auguste, M., and Yao, P.
RNA-binding proteins (RBPs) regulate the fate of RNA molecules, impacting posttranscriptional gene regulation processes. RBPs interact with RNAs through specific domains, influencing their splicing, transport, modification, translation, and degradation. Abnormalities in RBPs are linked to human disorders. Proline rich Coiled-coil 2B (PRRC2B) is an understudied RBP associated with cancer. Previous studies suggest that PRRC2B may be part of the translation initiation complex mediated by eukaryotic initiation factor 4G2 (eIF4G2). However, the exact function and mRNA targets of PRRC2B in translational regulation remain unknown. In this study, the researchers comprehensively characterized PRRC2B in translational regulation using human embryonic kidney (HEK293T) cells.
To assess changes in translation efficiency upon PRRC2B knockdown, the authors performed polysome profiling and RNA sequencing. RNA sequencing was performed on polysome-associated mRNAs and total mRNAs. They identified 1455 mRNAs with increased translation efficiency (TE-up) and 3197 mRNAs with decreased translation efficiency (TE-down) upon PRRC2B knockdown. Gene Ontology analysis revealed functional enrichments for TE-up genes in processes like pattern specification and mitochondrial transport, while TE-down genes were enriched in cytosolic transport and regulation of mRNA processing. Focusing on PRRC2B-bound mRNAs, they found that among the 223 mRNAs with PRRC2B binding sites, 18 showed increased TE and 80 showed decreased TE. These differentially translated PRRC2B-bound mRNAs were functionally enriched in processes such as cytoplasmic translation, ribosome assembly, stem cell population maintenance, and maintenance of cell number. Loss of PRRC2B binding leads to reduced translation efficiency of PRRC2B-bound mRNAs encoding oncogenes and cell cycle regulators, such as cyclin D2, resulting in impaired cell cycle progression.
Understanding the mechanisms of translational control mediated by PRRC2B provides insights into the regulation of gene expression and may have implications for cancer research and therapeutic strategies targeting dysregulated translation.
The ASC-1 complex promotes translation initiation by scanning ribosomes
The EMBO Journal, 2023
Kito, Y., Matsumoto, A., Ichihara, K., Shiraishi, C., Tang, R., Hatano, A., Matsumoto, M., Han, P., Iwasaki, S., and Nakayama, K.
Translation of mRNA in mammalian cells involves the binding of eIF4F to the mRNA’s cap structure, followed by the binding of the 43S preinitiation complex (PIC). This process requires eIF2, GTP, and Met-tRNAi to form the 43S PIC, which then recruits the 40S ribosomal subunit and the eIF3 complex. RNA helicases, such as eIF4A, DDX3, DHX9, and DHX36, play important roles in translation initiation by interacting with ribosomes or unwinding structured regions of mRNAs. In situations without stop codons or premature polyadenylation, the ribosome-associated quality control (RQC) pathway triggers translation arrest and degradation aberrant or stalled nascent polypeptides. The ASC-1 complex (ASCC) is a mammalian counterpart of the yeast RQT (Ribosome-associated Quality control complex) complex and is involved in disassembling disomes. The goal of this study was to investigate the role of the ASC-1 complex (ASCC) in translation initiation and its association with scanning ribosomes. The researchers aimed to identify components of eIF4A-bound scanning ribosomes and determine the function of ASCC in the regulation of translation initiation.
Ribosome profiling captures ribosomal elongation but not scanning ribosomes. Selective Translation Complex Profile Sequencing (Sel-TCP-seq) focuses on scanning ribosomes by capturing and analyzing ribosome-mRNA complexes. In this study, Sel-TCP-seq was combined with immunopurification to capture ribosomes associated with eIF4A1. The findings revealed that ASCC binds to both scanning and 80S ribosomes, expanding our understanding of translation initiation. These insights into the molecular mechanisms and regulation of translation initiation have implications for translational control and potential therapeutic targets. The study advances our knowledge of cellular processes and offers avenues for further research in modulating translation.
Evolutionary Trajectories of New Duplicated and Putative De Novo Genes
Molecular Biology & Evolution, 2023
Montañés, JC., Huertas, M., Messeguer, X., and Albá, M.
The evolution of new genes through gene duplication or de novo gene birth is crucial for evolutionary innovation and species adaptation. De novo genes originate from non-genic sequences, while gene duplication involves the replication of existing genes. De novo genes are smaller, have nonoptimal codon usage, positive charge, and transmembrane domains, whereas duplicated genes resemble their ancestors. Species-specific proteins, including de novo genes, are more abundant, indicating higher loss rates for younger genes. While both types of genes have higher evolutionary rates than house keeping genes, the extent of constraints relaxation and subsequent changes in evolution differ. Comparing properties in yeasts and flies helps understand these mechanisms better.
The study utilized ribosome profiling data to identify novel open reading frames (ORFs) with evidence of translation in Saccharomyces cerevisiae (S. cerevisiae) and Drosophila melanogaster (D. melanogaster). In S. cerevisiae, previously identified novel translated ORFs were used, while in D. melanogaster, ribosome profiling data from adult fly heads and S2 cells were analyzed. The data was mapped to transcriptomes, and ORFs meeting specific criteria were selected. These novel ORFs were added to the protein annotations for further analysis. The study employed ribosome profiling as a tool to discover novel translated ORFs into the understanding of gene expression in the two species.
The researchers found both gene duplication and de novo gene birth contribute to the formation of new genes. These new genes exhibit low sequence constraints and high turnover rates at the species level. Despite their different origins, both types of genes show similarities in their initial evolutionary phases. Putative de novo proteins undergo rapid changes, and there is a high level of genetic variation at the species level. Overall, this study enhances our understanding of gene formation and evolution.
