bims-micpro Biomed News
on Discovery and characterization of microproteins
Issue of 2023‒02‒26
seven papers selected by
Thomas Farid Martínez
University of California, Irvine

  1. Biomolecules. 2023 Jan 19. pii: 206. [Epub ahead of print]13(2):
      Primary transcripts of microRNAs (pri-miRNAs) were initially defined as long non-coding RNAs that host miRNAs further processed by the microRNA processor complex. A few years ago, however, it was discovered in plants that pri-miRNAs actually contain functional open reading frames (sORFs) that translate into small peptides called miPEPs, for microRNA-encoded peptides. Initially detected in Arabidopsis thaliana and Medicago truncatula, recent studies have revealed the presence of miPEPs in other pri-miRNAs as well as in other species ranging from various plant species to animals. This suggests that miPEP numbers remain largely underestimated and that they could be a common signature of pri-miRNAs. Here we present the most recent advances in miPEPs research and discuss how their discovery has broadened our vision of the regulation of gene expression by miRNAs, and how miPEPs could be interesting tools in sustainable agriculture or the treatment of certain human diseases.
    Keywords:  animal miPEP; microRNA; peptide; plant miPEP; sORF
  2. Mol Cell. 2023 Feb 14. pii: S1097-2765(23)00075-8. [Epub ahead of print]
      All species continuously evolve short open reading frames (sORFs) that can be templated for protein synthesis and may provide raw materials for evolutionary adaptation. We analyzed the evolutionary origins of 7,264 recently cataloged human sORFs and found that most were evolutionarily young and had emerged de novo. We additionally identified 221 previously missed sORFs potentially translated into peptides of up to 15 amino acids-all of which are smaller than the smallest human microprotein annotated to date. To investigate the bioactivity of sORF-encoded small peptides and young microproteins, we subjected 266 candidates to a mass-spectrometry-based interactome screen with motif resolution. Based on these interactomes and additional cellular assays, we can associate several candidates with mRNA splicing, translational regulation, and endocytosis. Our work provides insights into the evolutionary origins and interaction potential of young and small proteins, thereby helping to elucidate this underexplored territory of the human proteome.
    Keywords:  PRISMA; de novo genes; microproteins; primate-specific proteins; protein evolution; protein interactome; ribosome profiling; short ORFs; short linear motifs, SLiMs; short peptides
  3. iScience. 2023 Feb 17. 26(2): 106069
      Microproteins and short open reading frame-encoded peptides (SEPs) can, like all proteins, carry numerous posttranslational modifications. Together with posttranscriptional processes, this leads to a high number of possible distinct protein molecules, the proteoforms, out of a limited number of genes. The identification, quantification, and molecular characterization of proteoforms possess special challenges to established, mainly bottom-up proteomics (BUP) based analytical approaches. While BUP methods are powerful, proteins have to be inferred rather than directly identified, which hampers the detection of proteoforms. An alternative approach is top-down proteomics (TDP) which allows to identify intact proteoforms. This perspective article provides a brief overview of modified microproteins and SEPs, introduces the proteoform terminology, and compares present BUP and TDP workflows highlighting their major advantages and caveats. Necessary future developments in TDP to fully accentuate its potential for proteoform-centric analytics of microproteins and SEPs will be discussed.
    Keywords:  Biochemistry; Molecular biology; Molecular mechanism of gene regulation; Proteomics
  4. Proc Natl Acad Sci U S A. 2023 Feb 28. 120(9): e2221109120
      Certain long non-coding RNAs (lncRNAs) are known to contain small open reading frames that can be translated. Here we describe a much larger 25 kDa human protein, "Ribosomal IGS Encoded Protein" (RIEP), that remarkably is encoded by the well-characterized RNA polymerase (RNAP) II-transcribed nucleolar "promoter and pre-rRNA antisense" lncRNA (PAPAS). Strikingly, RIEP, which is conserved throughout primates but not found in other species, predominantly localizes to the nucleolus as well as mitochondria, but both exogenously expressed and endogenous RIEP increase in the nuclear and perinuclear regions upon heat shock (HS). RIEP associates specifically with the rDNA locus, increases levels of the RNA:DNA helicase Senataxin, and functions to sharply reduce DNA damage induced by heat shock. Proteomics analysis identified two mitochondrial proteins, C1QBP and CHCHD2, both known to have mitochondrial and nuclear functions, that we show interact directly, and relocalize following heat shock, with RIEP. Finally, it is especially notable that the rDNA sequences encoding RIEP are multifunctional, giving rise to an RNA that functions both as RIEP messenger RNA (mRNA) and as PAPAS lncRNA, as well as containing the promoter sequences responsible for rRNA synthesis by RNAP I. Our work has thus not only shown that a nucleolar "non-coding" RNA in fact encodes a protein, but also established a novel link between mitochondria and nucleoli that contributes to the cellular stress response.
    Keywords:  lncRNA; mitochondria; nucleolus; stress
  5. Diabetes Metab J. 2023 Feb 24.
      Mitochondria are complex metabolic organelles with manifold pathophysiological implications in diabetes. Currently published mitochondrial-encoded peptides, which are expressed from the mitochondrial open reading frame of the 12S ribosomal RNA type-c (MOTS-c), 16S rRNA (humanin and short humanin like peptide 1-6 [SHLP1-6]), or small human mitochondrial open reading frame over serine tRNA (SHMOOSE) are associated with regulation of cellular metabolism and insulin action in age-related diseases, such as type 2 diabetes mellitus. This review focuses mainly on recent advances in MOTS-c research with regards to diabetes, including both type 1 and type 2. The emerging understanding of MOTS-c in diabetes may provide insight into the development of new therapies for diabetes and other age or senescence-related diseases.
    Keywords:  Aging; Diabetes mellitus, type 2; Intracellular signaling peptides and proteins; Mitochondria
  6. Antioxidants (Basel). 2023 Feb 18. pii: 518. [Epub ahead of print]12(2):
      Mitochondrial open reading frame of the 12S rRNA type-c (MOTS-c) is the most unearthed peptide encoded by mitochondrial DNA (mtDNA). It is an important regulator of the nuclear genome during times of stress because it promotes an adaptive stress response to maintain cellular homeostasis. Identifying MOTS-c specific binding partners may aid in deciphering the complex web of mitochondrial and nuclear-encoded signals. Mitochondrial damage and dysfunction have been linked to aging and the accelerated cell death associated with many types of retinal degenerations. Furthermore, research on MOTS-c ability to revive oxidatively stressed RPE cells has revealed a significant protective role for the molecule. Evidence suggests that senescent cells play a role in the development of age-related retinal disorders. This review examines the links between MOTS-c, mitochondria, and age-related diseases of the retina. Moreover, the untapped potential of MOTS-c as a treatment for glaucoma, diabetic retinopathy, and age-related macular degeneration is reviewed.
    Keywords:  MOTS-c; age-related macular degeneration; diabetic retinopathy; glaucoma; mitochondrial dysfunction
  7. Kidney Int. 2023 Feb 15. pii: S0085-2538(23)00085-6. [Epub ahead of print]
      Progressive fibrosis is a hallmark of chronic kidney disease, but we lack effective treatments to halt this destructive process. Here, we describe that the mitochondrial micropeptide (peptides of no more than 100 amino acids) was recently identified from Mitoregulin (MOXI) representing a new class of eukaryotic regulators controlling kidney fibrosis. MOXI expression was found to be up-regulated in human fibrotic kidney disease, and this correlated with the degree of fibrosis and loss of kidney function. MOXI was expressed in the cytoplasm and mitochondria of cultured tubular epithelial cells and translocate to the nucleus upon Transforming Growth Factor-β1 stimulation. Deletion of Moxi protected mice against fibrosis and inflammation in the folic acid and unilateral ureteral obstruction models. As a potential molecular therapy, treatment with an antisense MOXI oligonucleotide effectively knocked-down MOXI expression and protected against kidney fibrosis in both models. Bimolecular fluorescence complementation identified the enzyme N-acetyltransferase 14 (Nat14) and transcription factor c-Jun as MOXI binding partners. The MOXI/Nat14/c-Jun complex enhances basal and Transforming Growth Factor-β1 induced collagen I gene promoter activity. Phosphorylation at T49 is required for MOXI nuclear localization and for complex formation with Nat14 and c-Jun. Furthermore, mice with a MoxiT49A point mutation were protected in the models of kidney fibrosis. Thus, our studies demonstrate a key role for the micropeptide MOXI in kidney fibrosis and identify a new function of MOXI in forming a transcriptional complex with Nat14 and c-Jun.
    Keywords:  Moxi; chronic kidney disease; micropeptide; renal fibrosis; renal inflammation