February 11th, 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, Zheng et al. used Ribo-seq to reveal how cancer relies on cryptic non-canonical open reading frames for growth. Jia et al. focus on the role of dysregulated mRNA translation machinery in cancer pathogenesis and how ribosome-inactivating proteins (RIPs) with potential therapeutic interventions can selectively inhibit protein synthesis in cancer cells. Antonov et al. report the function of rare UUA codon in Streptomyces bacteria and its potential role in phage regulatory translational bypassing mechanism.
CRISPR–Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames
Nature Structural & Molecular Biology, 2023
Zheng, C., Wei, Y., Zhang, P., Lin, K., He, D., Teng, H., Manyam, G., Zhang, Z., Liu, W., Lee, H.R.L. and Tang, X.
Cryptic non-canonical open reading frames (ncORFs) are sequences within a genome that have the potential to be translated into proteins but are not recognized by traditional gene annotation methods. These ORFs are termed “cryptic” because they are hidden within non-coding regions, untranslated regions (UTRs), or within alternative reading frames that overlap known protein coding ORFs. Their significance lies in their potential to encode functional peptides or small proteins that may play critical roles in cellular processes, disease development, or adaptation.
Traditional methods for identifying protein-coding genes often miss ncORFs, which are shorter and less well conserved. Ribosome profiling (ribo-seq) is currently the leading technique to predict the translation of ncORFs within the regions of RNA species that are traditionally considered noncoding.
In this study, the authors combined ribo-seq and a CRISPR-Cas9 knockout screen to identify cryptic ncORFs that may be functionally important in colorectal cancer (CRC). The findings showed that ncORFs, when disrupted with the CRISPR-Cas9 technique, inhibited cancer cell proliferation and tumour growth revealing that many such ORFs are upregulated in CRC compared to normal tissues.
One notable discovery was the microprotein SMIMP, encoded by the primate-specific long noncoding RNA ELFN1-AS1, which promotes tumor growth by interacting with SMC1A, a core subunit of the cohesin complex. This interaction facilitates the epigenetic repression of tumor-suppressive genes, highlighting the potential therapeutic or diagnostic significance of cryptic non-canonical ORFs in cancer.
The study highlights the importance of exploring unconventional aspects of the genome, such as ncORFs, in understanding cancer dependencies and developing new treatment strategies.
The role of dysregulated mRNA translation machinery in cancer pathogenesis and therapeutic value of ribosome-inactivating proteins
Biochimica et Biophysica Acta (BBA)-Reviews on Cancer, 2023
Jia, W., Yuan, J., Li, S. and Cheng, B.
The focus of this review is how the dysregulation of mRNA translation machinery which is a hallmark of cancer, contributes to tumour progression and therapy resistance. By sequencing ribosome-protected mRNA fragments (RPFs), ribo-seq enables the precise mapping of actively translated regions of the genome, thereby revealing dysregulated mRNA translation machinery in cancer cells. This technique helps identify aberrant translation initiation factors, elongation factors, and ribosomal proteins implicated in cancer pathogenesis. Hence ribo-seq can facilitate the exploration of potential therapeutic interventions, such as ribosome-inactivating proteins (RIPs), which selectively inhibit protein synthesis in cancer cells.
RIPs are a class of enzymes that inactivate ribosomes, thereby inhibiting protein synthesis. They do this by depurinating a specific adenine residue from the ribosomal RNA, which is crucial for the ribosome’s ability to translate mRNA into proteins. Their significance lies in their potential therapeutic applications, especially in cancer treatment, as they can selectively kill cancer cells by halting their protein production. RIPs are also explored for their use in creating immunotoxins for targeted therapy, where they are conjugated to antibodies that direct them specifically to cancer cells.
The review offered novel strategies for cancer treatment and highlights the therapeutic value of targeting dysregulated translation machinery. Additionally the review provides insights into the molecular mechanisms underlying cancer pathogenesis and proposes RIPs as a novel and effective approach for cancer treatment by targeting the dysregulated mRNA translation machinery.
Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing
RNA Biology, 2023
This research explored the functional role of the rare codon UUA in Streptomyces bacteria, investigating its association with adpA-related genes and its potential involvement in phage regulatory translational bypassing. The Streptomyces species are significant due to their remarkable ability to produce over two-thirds of clinically useful antibiotics, along with a multitude of immunosuppressants and anticancer agents.
The UUA codon is rare in Streptomyces and this work explores the role of the rare UUA codon in the adpA gene. The adpA gene in Streptomyces plays a pivotal role as a key transcriptional regulator within the A-factor regulatory cascade, which is essential for initiating and controlling the complex process of morphological differentiation and secondary metabolism, including antibiotic production.
Published Ribo-seq data revealed ribosome pausing at the conserved UUA codon upstream of the adpA start-codon. It suggested the potential role of UUA codons in phage regulatory translational bypassing, elucidating mechanisms by which bacteria respond to phage infections and adapt their gene expression. The regulation of the adpA gene may involve two UUA codons – an internal UUA and a UUA associated with a non-AUG initiated upstream ORF (uORF).
Interestingly, the authors report that while the analysed ribosome profiling (monosome-seq) data showed evidence of translation 5’ of the main ORF start, they cautioned about making more specific inferences with respect to collided ribosomes. They suggest that additional data such as disome and polysome profiling at different growth phases would be helpful.
The work emphasizes the role of the rare UUA codon in the adpA gene, which is crucial for transitioning between these phases. Through ribosome profiling data, the research reveals ribosome pausing at UUA codons, suggesting their significant role in gene expression regulation and potential implications for understanding bacterial cell cycle control and secondary metabolite production.