February 9th, 2025
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,
- Saito et al. find that DMDA-PatA inhibits eIF4A activity through a mechanism distinct from similarly-acting eIF4a inhibitors.
- Miao et al. find that glucose potentiates NSUN2 activity, driving enhanced translation of key pro-differentiation transcripts.
- Dopler et al. find that a distinct subpopulation of ribosomes defined by the P-stalk, which preferentially translate mRNAs related to cytokine response.
DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs
Nature Communications, 2024
Saito, H., Handa, Y., Chen, M., Schneider-Poetsch, T., Shichino, Y., Takahashi, M., Romo, D., Yoshida, M., Fürstner, A., Ito, T., Fukuzawa, K., and Iwasaki, S.
The production of harmful proteins is a key driver of many diseases, highlighting the therapeutic potential of compounds that modulate protein synthesis at the translational level. Despite the identification of several mRNA-selective translation inhibitors, their numbers remain limited, warranting further exploration. Natural secondary metabolites have been widely repurposed in drug development, including for translation inhibition. Compounds like hippuristanol, rocaglates, pateamine A, and sanguinarine target the eukaryotic translation initiation factor eIF4A, disrupting translation initiation via various mechanisms. Rocaglates clamp eIF4A to RNA motifs, while the precise mechanism of pateamine A remains unclear, necessitating further investigation into its action.
Ribosome profiling and RNA pulldown-Seq in HEK293 cells reveal that DMDA-PatA selectively clamps eIF4A onto GNG RNA motifs, causing mRNA-selective translation repression by sterically hindering ribosome scanning. Unlike other eIF4A inhibitors like RocA, which primarily target polypurine motifs, DMDA-PatA demonstrates a distinct preference for GNG motifs, facilitated by a positively charged tertiary amine on its trienyl arm. DMDA-PatA functions in an ATP-independent manner, enhancing the interaction of eIF4A with specific mRNAs, leading to their translational repression. It also targets the DEAD-box protein DDX3X, similarly clamping it to GNG motifs without affecting unrelated helicases like DDX6. Knockdown experiments confirm eIF4A1 and eIF4A2 as primary mediators of DMDA-PatA-induced cytotoxicity. These findings highlight DMDA-PatA’s potential for targeted translational control and its therapeutic relevance, particularly in cancers with DDX3X overexpression.
Learn more about EIRNA Bio’s ribosome profiling and RNA-seq services here.
Glucose binds and activates NSUN2 to promote translation and epidermal differentiation
Nucleic Acids Research, 2024
Miao, W., Porter, D.F., Li, Y., Meservey, L.M., Yang, Y.Y., Ma, C., Ferguson, I.D., Tien, V.B., Jack, T.M., Ducoli, L. and Lopez-Pajares, V.
Stratified epithelia, including the epidermis, protect organs and rely on basal cells differentiating into specialized suprabasal cells. This process, crucial for maintaining barrier function, involves dynamic gene regulation by transcription factors (TFs) and RNA-binding proteins (RBPs). Emerging evidence highlights glucose’s non-energetic roles in differentiation, particularly by modulating protein functions like IRF6 and DDX21 oligomerization. NSUN2, an RNA methyltransferase, supports epidermal stem cell differentiation and acts as a glucose sensor, enhancing its enzymatic activity. The glucose-NSUN2 interaction suggests a broader paradigm where glucose influences cellular differentiation by modulating protein activity, warranting further exploration of its regulatory mechanisms.
NSUN2-glucose binding was found to enhance its oligomerization, enzymatic activity, and RNA-binding specificity. Furthermore, glucose promotes NSUN2’s association with pro-differentiation mRNAs, particularly at 3′UTR m5C modification sites, and shifts its RNA interactions from intronic regions to exonic regions during keratinocyte differentiation. Ribosome profiling (Ribo-seq) demonstrated that NSUN2 depletion significantly decreases translational efficiency (TE) of pro-differentiation mRNAs without major changes in mRNA abundance, emphasizing its role in promoting protein synthesis. BioID experiments revealed glucose enhances NSUN2 interactions with translation-related proteins, including the ribosomal protein RPLP0. Functional studies confirmed that NSUN2 binding facilitates the translation of key differentiation-related mRNAs, such as GRHL3, which is critical for keratinocyte differentiation. Mutation of glucose-binding residues (K28/R29) in NSUN2 abolished its ability to enhance translation, underscoring the importance of glucose-mediated NSUN2 activation in regulating mRNA translation and its broader role in epidermal differentiation and translational control.
Learn more about EIRNA Bio’s ribosome profiling service here.
P-stalk ribosomes act as master regulators of cytokine-mediated processes
Cell, 2024
Dopler, A., Alkan, F., Malka, Y., van der Kammen, R., Hoefakker, K., Taranto, D., Kocabay, N., Mimpen, I., Ramirez, C., Malzer, E. and Isaeva, O.I.
Immune evasion is a hallmark of cancer, with cytokines like IFNγ and TNF-α playing pivotal roles in immune checkpoint blockade responses. While IFNγ enhances antigen presentation and immune activation, inhibitory cytokines like TGF-β suppress immune responses. Despite significant transcriptional insights, the post-transcriptional regulation of cytokine-induced tumor behavior remains underexplored. Emerging evidence suggests ribosomal heterogeneity and specialized ribosomal functions, such as the hypothesized “immunoribosome,” may drive antigenic peptide generation and cytokine responses. Ribosomal proteins are implicated in immune processes, including T cell and dendritic cell activation. This highlights a potential ribosome-mediated mechanism of cytokine-induced cellular rewiring in tumors.
The study identifies a cytokine-responsive ribosome subpopulation, termed the P-stalk ribosome (PSR), characterized by increased incorporation of P1 and P2 ribosomal proteins following exposure to immune-activating cytokines like IFNγ and TNF-α. This incorporation is linked to the regulation of antigen presentation processes (APP). Knockdown of P1 significantly reduced APP and impaired tumor cell recognition and killing by CD8+ T cells, without globally inhibiting protein synthesis. Ribosome profiling revealed that PSRs preferentially translate mRNAs critical for immunosurveillance, such as HLA and other APP components, with specificity driven by enrichment at transmembrane domains. PSR activation is a slow, cytokine-induced process, whereas TGF-β-mediated inhibition occurs rapidly via phosphorylation of P-stalk proteins. Phospho-dead mutants of P2 resist TGF-β-mediated suppression and maintain high APP levels. The PSR is conserved across cell types, species, and diverse tissues, highlighting its crucial role in modulating immune responses and antigen presentation in tumor immunology.
Learn more about EIRNA Bio’s ribosome profiling service here.