bims-micpro Biomed News
on Discovery and characterization of microproteins
Issue of 2020–07–05
nine papers selected by
Thomas Farid Martínez, University of California, Irvine
  1. [Junk DNA is out of fashion].
  2. Proteomic analysis of meiosis and characterization of novel short open reading frames in the fission yeast Schizosaccharomyces pombe.
  3. Sequential Precipitation and Delipidation Enables Efficient Enrichment of Low-Molecular Weight Proteins and Peptides from Human Plasma.
  4. Quantification of translation uncovers the functions of the alternative transcriptome.
  5. When the Smoke Clears m6A from a Y Chromosome-Linked lncRNA, Men Get an Increased Risk of Cancer.
  6. Promiscuous Binding of Microprotein Mozart1 to γ-Tubulin Complex Mediates Specific Subcellular Targeting to Control Microtubule Array Formation.
  7. MetaRibo-Seq measures translation in microbiomes.
  8. Using AnABlast for intergenic sORF prediction in the C. elegans genome.
  9. Uncovering small membrane proteins in pathogenic bacteria: regulatory functions and therapeutic potential.
  1. Med Sci (Paris). 2020 Jun-Jul;36(6-7):36(6-7): 675-677
    [Junk DNA is out of fashion].
    Bertrand Jordan.
      A systematic search for non-conventional open reading frames in human DNA reveals a large number of small ORFs encoding peptides generally smaller than 100 amino-acids. These ORFs are transcribed and translated into small proteins, which are demonstrated to have functional significance by bulk CRISPR inactivation. Evidence is also found for bicistronic mRNAs including such a small ORF upstream of a canonical coding sequence. These findings add a new facet to our understanding of biological processes.
    DOI:  https://doi.org/10.1051/medsci/2020108
  2. Cell Cycle. 2020 Jun 17. 1-9
    Proteomic analysis of meiosis and characterization of novel short open reading frames in the fission yeast Schizosaccharomyces pombe.
    Barbora Huraiova, Judit Kanovits, Silvia Bagelova Polakova, Lubos Cipak, Zsigmond Benko, Andrea Sevcovicova, Dorothea Anrather, Gustav Ammerer, Caia D S Duncan, Juan Mata, Juraj Gregan.
      Meiosis is the process by which haploid gametes are produced from diploid precursor cells. We used stable isotope labeling by amino acids in cell culture (SILAC) to characterize the meiotic proteome in the fission yeast Schizosaccharomyces pombe. We compared relative levels of proteins extracted from cells harvested around meiosis I with those of meiosis II, and proteins from premeiotic S phase with the interval between meiotic divisions, when S phase is absent. Our proteome datasets revealed peptides corresponding to short open reading frames (sORFs) that have been previously identified by ribosome profiling as new translated regions. We verified expression of selected sORFs by Western blotting and analyzed the phenotype of deletion mutants. Our data provide a resource for studying meiosis that may help understand differences between meiosis I and meiosis II and how S phase is suppressed between the two meiotic divisions.
    Keywords:  Meiosis; fission yeast Schizosaccharomyces pombe ; short open reading frames; silac
    DOI:  https://doi.org/10.1080/15384101.2020.1779470
  3. J Proteome Res. 2020 Jul 03.
    Sequential Precipitation and Delipidation Enables Efficient Enrichment of Low-Molecular Weight Proteins and Peptides from Human Plasma.
    Na Li, Yue Zhou, Jifeng Wang, Lili Niu, Qing Zhang, Lang Sun, Xiang Ding, Xiaojing Guo, Zhensheng Xie, Nali Zhu, Mengmeng Zhang, Xiulan Chen, Tanxi Cai, Fuquan Yang.
      Low-molecular weight proteins and peptides (LMWPs, <30 kDa) in human plasma serve as potential biomarkers or drug targets and are endowed with desirable traits for biological and clinical studies. However, the identification of LMWPs from plasma is retarded by high-abundance proteins, high-molecular weight proteins, and lipids. Here, we present a sequential precipitation and delipidation (SPD) method for the efficient enrichment of LMWPs based on methyl-tert-butyl ether/methanol/water systems. The enriched LMWP sample was analyzed by single-shot liquid chromatography-tandem mass spectrometry employing both HCD and EThcD without tryptic digestion, and 725 peptides were identified on average. The LMWP sample was also digested and analyzed using a bottom-up proteomics pipeline, and 289 proteins were identified, of which 129 (44.6%) proteins were less than 30 kDa and lipoprotein-associated proteins were significantly enriched. Additionally, 25 neuropeptides and 19 long noncoding RNA-encoded polypeptides were identified. Taken together, the SPD method shows good sensitivity and reproducibility when compared with other enrichment methods and has great potential for clinical biomarker discovery and application.
    Keywords:  SPD; bottom-up proteomics; lipoproteins; low-molecular weight proteins and peptides; neuropeptides; peptidomics; smORF-encoded polypeptides
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00232
  4. Nat Struct Mol Biol. 2020 Jun 29.
    Quantification of translation uncovers the functions of the alternative transcriptome.
    Lorenzo Calviello, Antje Hirsekorn, Uwe Ohler.
      Translation has a fundamental function in defining the fate of the transcribed genome. RNA-sequencing (RNA-seq) data enable the quantification of complex transcript mixtures, often detecting several transcript isoforms of unknown functions for one gene. Here, we describe ORFquant, a method to annotate and quantify translation at the level of single open reading frames (ORFs), using information from Ribo-seq data. By developing an approach for transcript filtering, we quantify translation transcriptome-wide, revealing translated ORFs on multiple isoforms per gene. For most genes, one ORF represents the dominant translation product, but we also detect genes with translated ORFs on multiple transcript isoforms, including targets of RNA surveillance mechanisms. Measuring translation across human cell lines reveals the extent of gene-specific differences in protein production, supported by steady-state protein abundance estimates. Computational analysis of Ribo-seq data with ORFquant ( https://github.com/lcalviell/ORFquant ) provides insights into the heterogeneous functions of complex transcriptomes.
    DOI:  https://doi.org/10.1038/s41594-020-0450-4
  5. Cancer Res. 2020 Jul 01. 80(13): 2718-2719
    When the Smoke Clears m6A from a Y Chromosome-Linked lncRNA, Men Get an Increased Risk of Cancer.
    A Rouf Banday, Brenen W Papenberg, Ludmila Prokunina-Olsson.
      Long noncoding RNAs (lncRNA) have been implicated in many diseases, including cancer. Although these disease-associated effects have been mostly attributed to the ability of lncRNAs to function as regulatory noncoding transcripts, there is growing evidence that lncRNAs may also encode functional micropeptides. In the current issue of Cancer Research, Wu and colleagues report a micropeptide encoded by a Y chromosome-linked lncRNA that may explain the higher incidence of esophageal cancer in male smokers. Furthermore, this report provides broader insights related to the molecular epidemiology of male-dominant and smoking-driven cancers and may also help explain some cancer-related associations with mosaic Y chromosome loss.See related article by Wu et al., p. 2790.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-0961
  6. Cell Rep. 2020 Jun 30. pii: S2211-1247(20)30817-2. [Epub ahead of print]31(13): 107836
    Promiscuous Binding of Microprotein Mozart1 to γ-Tubulin Complex Mediates Specific Subcellular Targeting to Control Microtubule Array Formation.
    Tzu-Lun Huang, Hsiu-Jung Wang, Ya-Chieh Chang, Shao-Win Wang, Kuo-Chiang Hsia.
      How γ-tubulin ring complex (γ-TuRC), a master template for microtubule nucleation, is spatially and temporally regulated for the assembly of new microtubule arrays remains unclear. Here, we report that an evolutionarily conserved microprotein, Mozart1 (Mzt1), regulates subcellular targeting and microtubule formation activity of γ-TuRC at different cell cycle stages. Crystal structures of protein complexes demonstrate that Mzt1 promiscuously interacts with the N-terminal domains of multiple γ-tubulin complex protein subunits in γ-TuRC via an intercalative binding mode. Genetic- and microscopy-based analyses show that promiscuous binding of Mzt1 in γ-TuRC controls specific subcellular localization of γ-TuRC to modulate microtubule nucleation and stabilization in fission yeast. Moreover, we find Mzt1-independent targeting of γ-TuRC to be crucial for mitotic spindle assembly, demonstrating the cell-cycle-dependent regulation and function of γ-TuRC. Our findings reveal a microprotein-mediated regulatory mechanism underlying microtubule cytoskeleton formation, whereby Mzt1 binding promiscuity confers localization specificity on the multi-protein complex γ-TuRC.
    Keywords:  Mozart1; microprotein; microtubule nucleation; γ-TuRC; γ-TuRC targeting
    DOI:  https://doi.org/10.1016/j.celrep.2020.107836
  7. Nat Commun. 2020 Jun 29. 11(1): 3268
    MetaRibo-Seq measures translation in microbiomes.
    Brayon J Fremin, Hila Sberro, Ami S Bhatt.
      No method exists to measure large-scale translation of genes in uncultured organisms in microbiomes. To overcome this limitation, we develop MetaRibo-Seq, a method for simultaneous ribosome profiling of tens to hundreds of organisms in microbiome samples. MetaRibo-Seq was benchmarked against gold-standard Ribo-Seq in a mock microbial community and applied to five different human fecal samples. Unlike RNA-Seq, Ribo-Seq signal of a predicted gene suggests it encodes a translated protein. We demonstrate two applications of this technique: First, MetaRibo-Seq identifies small genes, whose identification until now has been challenging. For example, MetaRibo-Seq identifies 2,091 translated, previously unannotated small protein families from five fecal samples, more than doubling the number of small proteins predicted to exist in this niche. Second, the combined application of RNA-Seq and MetaRibo-Seq identifies differences in the translation of transcripts. In summary, MetaRibo-Seq enables comprehensive translational profiling in microbiomes and identifies previously unannotated small proteins.
    DOI:  https://doi.org/10.1038/s41467-020-17081-z
  8. Bioinformatics. 2020 Jul 02. pii: btaa608. [Epub ahead of print]
    Using AnABlast for intergenic sORF prediction in the C. elegans genome.
    C S Casimiro-Soriguer, M M Rigual, A M Brokate-Llanos, M J Muñoz, A Garzón, A J Pérez-Pulido, J Jimenez.
       MOTIVATION: Short bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance.
    RESULTS: AnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. This protein-coding finder is independent of ORF length and reading frame shifts, thus making of AnABlast a potentially useful tool to predict sORFs. By using this algorithm, here we report the identification of 82 putative new intergenic sORFs in the Caenorhabditis elegans genome. Sequence similarity, motif presence, expression data and RNA interference experiments support that the underlined sORFs likely encode functional peptides, encouraging the use of AnABlast as a new approach for the accurate prediction of intergenic sORFs in annotated eukaryotic genomes.
    AVAILABILITY: AnABlast is freely available at http://www.bioinfocabd.upo.es/ab/. The C. elegans genome browser with AnABlast results, annotated genes, and all data used in this study is available at http://www.bioinfocabd.upo.es/celegans.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa608
  9. Mol Microbiol. 2020 Jun 29.
    Uncovering small membrane proteins in pathogenic bacteria: regulatory functions and therapeutic potential.
    Preeti Garai, Anne Blanc-Potard.
      Bacterial small proteins (below 50 amino acids) encoded by small open reading frames (sORFs) are recognized as an emerging class of functional molecules that have been largely overlooked in the past. While some were uncovered serendipitously, global approaches have recently been developed to detect these sORFs. A large portion of small proteins appears to be hydrophobic and located in the bacterial membrane. In the present review, we describe functional small hydrophobic proteins discovered in pathogenic bacteria and report recent advances in the discovery of additional ones. Small membrane proteins contribute to bacterial adaptation to changing environments and often appear to be implicated in negative feedback regulation loops by modulating the function or stability of larger membrane proteins. A subset of these proteins belongs to toxin-antitoxin modules. We highlight features of characterized hydrophobic small proteins that may pave the way for identification of the functional small proteins among novel sORFs discovered. Besides providing new insights into bacterial pathogenesis, identification of naturally-occuring small hydrophobic proteins of pathogenic bacteria can lead to new therapeutic interventions, as recently shown with the development of synthetic peptides derived from natural small proteins that display antibacterial or antivirulence properties.
    Keywords:  Small protein; antibacterial molecule; membrane protein; pathogenic bacteria; regulation
    DOI:  https://doi.org/10.1111/mmi.14564
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