bims-micpro 2020-09-20 papers

Issue of 2020‒09‒20
six papers selected by
Thomas Martinez
Salk Institute for Biological Studies

Mol Cancer. 2020 Sep 14. 19(1): 143

Identification of miPEP133 as a novel tumor-suppressor microprotein encoded by miR-34a pri-miRNA.

Min Kang, Bo Tang, Jixi Li, Ziyan Zhou, Kang Liu, Rensheng Wang, Ziyan Jiang, Fangfang Bi, David Patrick, Dongin Kim, Anirban K Mitra, Yang Yang-Hartwich.

BACKGROUND: Very few proteins encoded by the presumed non-coding RNA transcripts have been identified. Their cellular functions remain largely unknown. This study identifies the tumor-suppressor function of a novel microprotein encoded by the precursor of miR-34a. It consists of 133 amino acid residues, thereby named as miPEP133 (pri-microRNA encoded peptide 133).METHODS: We overexpressed miPEP133 in nasopharyngeal carcinoma (NPC), ovarian cancer and cervical cancer cell lines to determine its effects on cell growth, apoptosis, migration, or invasion. Its impact on tumor growth was evaluated in a xenograft NPC model. Its prognostic value was analyzed using NPC clinical samples. We also conducted western blot, immunoprecipitation, mass spectrometry, confocal microscopy and flow cytometry to determine the underlying mechanisms of miPEP133 function and regulation.
RESULTS: miPEP133 was expressed in normal human colon, stomach, ovary, uterus and pharynx. It was downregulated in cancer cell lines and tumors. miPEP133 overexpression induced apoptosis in cancer cells and inhibited their migration and invasion. miPEP133 inhibited tumor growth in vivo. Low miPEP133 expression was an unfavorable prognostic marker associated with advanced metastatic NPC. Wild-type p53 but not mutant p53 induced miPEP133 expression. miPEP133 enhanced p53 transcriptional activation and miR-34a expression. miPEP133 localized in the mitochondria to interact with mitochondrial heat shock protein 70kD (HSPA9) and prevent HSPA9 from interacting with its binding partners, leading to the decrease of mitochondrial membrane potential and mitochondrial mass.
CONCLUSION: miPEP133 is a tumor suppressor localized in the mitochondria. It is a potential prognostic marker and therapeutic target for multiple types of cancers.

Keywords: Nasopharyngeal carcinoma; Pri-miRNA-encoded protein; Tumor suppressor; miPEP133; miR-34a

DOI: https://doi.org/10.1186/s12943-020-01248-9

Nat Commun. 2020 09 16. 11(1): 4676

DENR promotes translation reinitiation via ribosome recycling to drive expression of oncogenes including ATF4.

Jonathan Bohlen, Liza Harbrecht, Saioa Blanco, Katharina Clemm von Hohenberg, Kai Fenzl, Günter Kramer, Bernd Bukau, Aurelio A Teleman.

Translation efficiency varies considerably between different mRNAs, thereby impacting protein expression. Translation of the stress response master-regulator ATF4 increases upon stress, but the molecular mechanisms are not well understood. We discover here that translation factors DENR, MCTS1 and eIF2D are required to induce ATF4 translation upon stress by promoting translation reinitiation in the ATF4 5'UTR. We find DENR and MCTS1 are only needed for reinitiation after upstream Open Reading Frames (uORFs) containing certain penultimate codons, perhaps because DENR•MCTS1 are needed to evict only certain tRNAs from post-termination 40S ribosomes. This provides a model for how DENR and MCTS1 promote translation reinitiation. Cancer cells, which are exposed to many stresses, require ATF4 for survival and proliferation. We find a strong correlation between DENR•MCTS1 expression and ATF4 activity across cancers. Furthermore, additional oncogenes including a-Raf, c-Raf and Cdk4 have long uORFs and are translated in a DENR•MCTS1 dependent manner.

DOI: https://doi.org/10.1038/s41467-020-18452-2

Nat Commun. 2020 09 16. 11(1): 4677

Translational induction of ATF4 during integrated stress response requires noncanonical initiation factors eIF2D and DENR.

Deepika Vasudevan, Sarah D Neuman, Amy Yang, Lea Lough, Brian Brown, Arash Bashirullah, Timothy Cardozo, Hyung Don Ryoo.

The Integrated Stress Response (ISR) helps metazoan cells adapt to cellular stress by limiting the availability of initiator methionyl-tRNA for translation. Such limiting conditions paradoxically stimulate the translation of ATF4 mRNA through a regulatory 5' leader sequence with multiple upstream Open Reading Frames (uORFs), thereby activating stress-responsive gene expression. Here, we report the identification of two critical regulators of such ATF4 induction, the noncanonical initiation factors eIF2D and DENR. Loss of eIF2D and DENR in Drosophila results in increased vulnerability to amino acid deprivation, susceptibility to retinal degeneration caused by endoplasmic reticulum (ER) stress, and developmental defects similar to ATF4 mutants. eIF2D requires its RNA-binding motif for regulation of 5' leader-mediated ATF4 translation. Consistently, eIF2D and DENR deficient human cells show impaired ATF4 protein induction in response to ER stress. Altogether, our findings indicate that eIF2D and DENR are critical mediators of ATF4 translational induction and stress responses in vivo.

DOI: https://doi.org/10.1038/s41467-020-18453-1

Nucleic Acids Res. 2020 Sep 17. pii: gkaa728. [Epub ahead of print]

eIF4G-driven translation initiation of downstream ORFs in mammalian cells.

Risa Nobuta, Kodai Machida, Misaki Sato, Satoshi Hashimoto, Yasuhito Toriumi, Shizuka Nakajima, Daiki Suto, Hiroaki Imataka, Toshifumi Inada.

Comprehensive genome-wide analysis has revealed the presence of translational elements in the 3' untranslated regions (UTRs) of human transcripts. However, the mechanisms by which translation is initiated in 3' UTRs and the physiological function of their products remain unclear. This study showed that eIF4G drives the translation of various downstream open reading frames (dORFs) in 3' UTRs. The 3' UTR of GCH1, which encodes GTP cyclohydrolase 1, contains an internal ribosome entry site (IRES) that initiates the translation of dORFs. An in vitro reconstituted translation system showed that the IRES in the 3' UTR of GCH1 required eIF4G and conventional translation initiation factors, except eIF4E, for AUG-initiated translation of dORFs. The 3' UTR of GCH1-mediated translation was resistant to the mTOR inhibitor Torin 1, which inhibits cap-dependent initiation by increasing eIF4E-unbound eIF4G. eIF4G was also required for the activity of various elements, including polyU and poliovirus type 2, a short element thought to recruit ribosomes by base-pairing with 18S rRNA. These findings indicate that eIF4G mediates translation initiation of various ORFs in mammalian cells, suggesting that the 3' UTRs of mRNAs may encode various products.

DOI: https://doi.org/10.1093/nar/gkaa728

Bioinformatics. 2020 Sep 14. pii: btaa783. [Epub ahead of print]

Annotating high-impact 5'untranslated region variants with the UTRannotator.

Xiaolei Zhang, Matthew Wakeling, James Ware, Nicola Whiffin.

SUMMARY: Current tools to annotate the predicted effect of genetic variants are heavily biased towards protein-coding sequence. Variants outside of these regions may have a large impact on protein expression and/or structure and can lead to disease, but this effect can be challenging to predict. Consequently, these variants are poorly annotated using standard tools. We have developed a plugin to the Ensembl Variant Effect Predictor, the UTRannotator, that annotates variants in 5'untranslated regions (5'UTR) that create or disrupt upstream open reading frames (uORFs). We investigate the utility of this tool using the ClinVar database, providing an annotation for 31.9% of all 5'UTR (likely) pathogenic variants, and highlighting 31 variants of uncertain significance as candidates for further follow-up. We will continue to update the UTRannotator as we gain new knowledge on the impact of variants in UTRs.AVAILABILITY AND IMPLEMENTATION: UTRannotator is freely available on Github: https://github.com/ImperialCardioGenetics/UTRannotator.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btaa783

Front Mol Biosci. 2020 ;7 187

Are Antisense Proteins in Prokaryotes Functional?

Zachary Ardern, Klaus Neuhaus, Siegfried Scherer.

Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ribosome profiling data. Determining the functional fraction of these protein products awaits further research, including insights from studies of molecular interactions and detailed evolutionary analysis. There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few. These proteins should be added to genome annotations, and the methods for predicting them standardized. Evolutionary analysis of these typically young sequences also may provide important insights into gene evolution. This research should be prioritized for its exciting potential to uncover large numbers of novel proteins with extremely diverse potential practical uses, including applications in synthetic biology and responding to pathogens.

Keywords: antisense transcription; antisense translation; function; gene annotation; overlapping gene; selected effects

DOI: https://doi.org/10.3389/fmolb.2020.00187