bims-micpro Biomed News
on Discovery and characterization of microproteins
Issue of 2021–08–29
six papers selected by
Thomas Farid Martínez, University of California, Irvine
  1. Investigation of LINC00493/SMIM26 Gene Suggests Its Dual Functioning at mRNA and Protein Level.
  2. Nothing Regular about the Regulins: Distinct Functional Properties of SERCA Transmembrane Peptide Regulatory Subunits.
  3. Structured elements drive extensive circular RNA translation.
  4. From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory.
  5. The Role of Mitochondria-Derived Peptides in Cardiovascular Diseases and Their Potential as Therapeutic Targets.
  6. Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells.
  1. Int J Mol Sci. 2021 Aug 06. pii: 8477. [Epub ahead of print]22(16):
    Investigation of LINC00493/SMIM26 Gene Suggests Its Dual Functioning at mRNA and Protein Level.
    Daria Konina, Peter Sparber, Iuliia Viakhireva, Alexandra Filatova, Mikhail Skoblov.
      The amount of human long noncoding RNA (lncRNA) genes is comparable to protein-coding; however, only a small number of lncRNAs are functionally annotated. Previously, it was shown that lncRNAs can participate in many key cellular processes, including regulation of gene expression at transcriptional and post-transcriptional levels. The lncRNA genes can contain small open reading frames (sORFs), and recent studies demonstrated that some of the resulting short proteins could play an important biological role. In the present study, we investigate the widely expressed lncRNA LINC00493. We determine the structure of the LINC00493 transcript, its cell localization and influence on cell physiology. Our data demonstrate that LINC00493 has an influence on cell viability in a cell-type-specific manner. Furthermore, it was recently shown that LINC00493 has a sORF that is translated into small protein SMIM26. The results of our knockdown and overexpression experiments suggest that both LINC00493/SMIM26 transcript and protein affect cell viability, but in the opposite manner.
    Keywords:  LINC00493; MTT; SMIM26; lncRNA; long noncoding RNA; sORF; wound healing
    DOI:  https://doi.org/10.3390/ijms22168477
  2. Int J Mol Sci. 2021 Aug 18. pii: 8891. [Epub ahead of print]22(16):
    Nothing Regular about the Regulins: Distinct Functional Properties of SERCA Transmembrane Peptide Regulatory Subunits.
    Nishadh Rathod, Jessi J Bak, Joseph O Primeau, M'Lynn E Fisher, Lennane Michel Espinoza-Fonseca, Mary Joanne Lemieux, Howard S Young.
      The sarco-endoplasmic reticulum calcium ATPase (SERCA) is responsible for maintaining calcium homeostasis in all eukaryotic cells by actively transporting calcium from the cytosol into the sarco-endoplasmic reticulum (SR/ER) lumen. Calcium is an important signaling ion, and the activity of SERCA is critical for a variety of cellular processes such as muscle contraction, neuronal activity, and energy metabolism. SERCA is regulated by several small transmembrane peptide subunits that are collectively known as the "regulins". Phospholamban (PLN) and sarcolipin (SLN) are the original and most extensively studied members of the regulin family. PLN and SLN inhibit the calcium transport properties of SERCA and they are required for the proper functioning of cardiac and skeletal muscles, respectively. Myoregulin (MLN), dwarf open reading frame (DWORF), endoregulin (ELN), and another-regulin (ALN) are newly discovered tissue-specific regulators of SERCA. Herein, we compare the functional properties of the regulin family of SERCA transmembrane peptide subunits and consider their regulatory mechanisms in the context of the physiological and pathophysiological roles of these peptides. We present new functional data for human MLN, ELN, and ALN, demonstrating that they are inhibitors of SERCA with distinct functional consequences. Molecular modeling and molecular dynamics simulations of SERCA in complex with the transmembrane domains of MLN and ALN provide insights into how differential binding to the so-called inhibitory groove of SERCA-formed by transmembrane helices M2, M6, and M9-can result in distinct functional outcomes.
    Keywords:  DWORF; SERCA; another-regulin; calcium transport; endoregulin; myoregulin; phospholamban; sarco-endoplasmic reticulum; sarcolipin
    DOI:  https://doi.org/10.3390/ijms22168891
  3. Mol Cell. 2021 Aug 19. pii: S1097-2765(21)00626-2. [Epub ahead of print]
    Structured elements drive extensive circular RNA translation.
    Chun-Kan Chen, Ran Cheng, Janos Demeter, Jin Chen, Shira Weingarten-Gabbay, Lihua Jiang, Michael P Snyder, Jonathan S Weissman, Eran Segal, Peter K Jackson, Howard Y Chang.
      The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs require internal ribosome entry sites (IRES) if they are to undergo translation without a 5' cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify more than 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue-specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is downregulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress. Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.
    Keywords:  18S complementarity; FGFR1; cap-independent translation; circFGFR1p; circRNA-encoded protein; circular RNA; internal ribosome entry site; structured RNA element
    DOI:  https://doi.org/10.1016/j.molcel.2021.07.042
  4. Noncoding RNA. 2021 Jul 27. pii: 44. [Epub ahead of print]7(3):
    From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory.
    Sara Andjus, Antonin Morillon, Maxime Wery.
      The Nonsense-Mediated mRNA Decay (NMD) has been classically viewed as a translation-dependent RNA surveillance pathway degrading aberrant mRNAs containing premature stop codons. However, it is now clear that mRNA quality control represents only one face of the multiple functions of NMD. Indeed, NMD also regulates the physiological expression of normal mRNAs, and more surprisingly, of long non-coding (lnc)RNAs. Here, we review the different mechanisms of NMD activation in yeast and mammals, and we discuss the molecular bases of the NMD sensitivity of lncRNAs, considering the functional roles of NMD and of translation in the metabolism of these transcripts. In this regard, we describe several examples of functional micropeptides produced from lncRNAs. We propose that translation and NMD provide potent means to regulate the expression of lncRNAs, which might be critical for the cell to respond to environmental changes.
    Keywords:  Upf1; lncRNA; micropeptide; nonsense-mediated mRNA decay; translation
    DOI:  https://doi.org/10.3390/ncrna7030044
  5. Int J Mol Sci. 2021 Aug 16. pii: 8770. [Epub ahead of print]22(16):
    The Role of Mitochondria-Derived Peptides in Cardiovascular Diseases and Their Potential as Therapeutic Targets.
    Siarhei A Dabravolski, Nikita G Nikiforov, Antonina V Starodubova, Tatyana V Popkova, Alexander N Orekhov.
      Mitochondria-derived peptides (MDPs) are small peptides hidden in the mitochondrial DNA, maintaining mitochondrial function and protecting cells under different stresses. Currently, three types of MDPs have been identified: Humanin, MOTS-c and SHLP1-6. MDPs have demonstrated anti-apoptotic and anti-inflammatory activities, reactive oxygen species and oxidative stress-protecting properties both in vitro and in vivo. Recent research suggests that MDPs have a significant cardioprotective role, affecting CVDs (cardiovascular diseases) development and progression. CVDs are the leading cause of death globally; this term combines disorders of the blood vessels and heart. In this review, we focus on the recent progress in understanding the relationships between MDPs and the main cardiovascular risk factors (atherosclerosis, insulin resistance, hyperlipidaemia and ageing). We also will discuss the therapeutic application of MDPs, modified and synthetic MDPs, and their potential as novel biomarkers and therapeutic targets.
    Keywords:  Humanin; MOTS-c; SHLPs; ageing; atherosclerosis; cardiovascular diseases; hyperlipidaemia; insulin resistance; mitochondria-derived peptides
    DOI:  https://doi.org/10.3390/ijms22168770
  6. Biomedicines. 2021 Jul 29. pii: 911. [Epub ahead of print]9(8):
    Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells.
    Joana Silva, Pedro Nina, Luísa Romão.
      ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5'-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5'-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments.
    Keywords:  ABCE1; colorectal cancer; translational regulation; uORFs
    DOI:  https://doi.org/10.3390/biomedicines9080911
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