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The role of micropeptides in biology

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Abstract

Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.

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References

  1. Dewitte M (2018) Computational protein discovery: can novel insights in the human transcriptome help us understand our genome? (eds) Ghent University. https://lib.ugent.be/fulltxt/RUG01/002/508/664/RUG01-002508664_2018_0001_AC.pdf

  2. Kornienko AE, Dotter CP, Guenzl PM, Gisslinger H, Gisslinger B, Cleary C, Kralovics R, Pauler FM, Barlow DP (2016) Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biol 17(1):14

    PubMed  PubMed Central  Google Scholar 

  3. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789. https://doi.org/10.1101/gr.132159.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Yin X, Hu J, Xu H (2018) Distribution of micropeptide-coding sORFs in transcripts. Chin Chem Lett 29(7):1029–1032

    CAS  Google Scholar 

  5. Chekulaeva M, Rajewsky N (2019) Roles of long noncoding RNAs and circular RNAs in translation. Cold Spring Harbor Perspect Biol 11(6):a032680

    CAS  Google Scholar 

  6. Waldron D (2015) Genomics: identification of sORFs. Nat Rev Genet 16(11):626

    Google Scholar 

  7. Olexiouk V, Crappé J, Verbruggen S, Verhegen K, Martens L, Menschaert G (2015) sORFs.org: a repository of small ORFs identified by ribosome profiling. Nucleic Acids Res 44(D1):D324–D329

    PubMed  PubMed Central  Google Scholar 

  8. Makarewich CA, Olson EN (2017) Mining for micropeptides. Trends Cell Biol 27(9):685–696

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Sousa ME, Farkas MH (2018) Micropeptide. PLoS Genet 14(12):e1007764

    PubMed  PubMed Central  Google Scholar 

  10. Plaza S, Menschaert G, Payre F (2017) In search of lost small peptides. Annu Rev Cell Dev Biol 33:391–416

    CAS  PubMed  Google Scholar 

  11. Drwiega J, Wang K, Shen T, Chaffin C, Youngblood P, Hardy R (2016) The significance of protein concentration on UPEP and UIFE analysis.: [51]. Ann Clin Lab Sci 46(3):331–332

    Google Scholar 

  12. Dumesic PA, Egan DF, Gut P, Tran MT, Parisi A, Chatterjee N, Jedrychowski M, Paschini M, Kazak L, Wilensky SE (2019) An evolutionarily conserved uORF regulates PGC1α and oxidative metabolism in mice, flies, and bluefin tsuna. Cell Metab 30:190–200

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Mortz M, Dégletagne C, Romestaing C, Duchamp C (2020) Comparative genomic analysis identifies small open reading frames (sORFs) with peptide-encoding features in avian 16S rDNA. Genomics 112(2):1120–1127

    CAS  PubMed  Google Scholar 

  14. Anderson DM, Anderson KM, Chang C-L, Makarewich CA, Nelson BR, McAnally JR, Kasaragod P, Shelton JM, Liou J, Bassel-Duby R (2015) A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160(4):595–606

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Chu Q, Martinez TF, Novak SW, Donaldson CJ, Tan D, Vaughan JM, Chang T, Diedrich JK, Andrade L, Kim A, Zhang T, Manor U, Saghatelian A (2019) Regulation of the ER stress response by a mitochondrial microprotein. Nat Commun 10(1):4883. https://doi.org/10.1038/s41467-019-12816-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Cai B, Li Z, Ma M, Wang Z, Han P, Abdalla BA, Nie Q, Zhang X (2017) LncRNA-Six1 encodes a micropeptide to activate Six1 in Cis and is involved in cell proliferation and muscle growth. Front Physiol 8:230

    PubMed  PubMed Central  Google Scholar 

  17. Anderson DM, Makarewich CA, Anderson KM, Shelton JM, Bezprozvannaya S, Bassel-Duby R, Olson EN (2016) Widespread control of calcium signaling by a family of SERCA-inhibiting micropeptides. Sci Signal 9(457):ra119

    PubMed  PubMed Central  Google Scholar 

  18. Singh DR, Cho E, Dalton M, Pribadi M, Makarewich CA, Olson EN, Robia SL (2019) Oligomerization of micropeptides that regulate SERCA. Biophys J 116(3):30a–31a

    Google Scholar 

  19. Morozov SY, Ryazantsev DY, Tatiana NE (2019) Bioinformatics analysis of the novel conserved micropeptides encoded by the plants of family Brassicaceae. J Bioinform and Syst Biol 2:066–077

    Google Scholar 

  20. Olexiouk V, Menschaert G (2016) Identification of small novel coding sequences, a proteogenomics endeavor. In: Végvári Á. (eds) Proteogenomics. Advances in experimental medicine and biology, vol 926. Springer, Cham

  21. Li Y, Chen X, Sun H, Wang H (2018) Long non-coding RNAs in the regulation of skeletal myogenesis and muscle diseases. Cancer Lett 417:58–64

    CAS  PubMed  Google Scholar 

  22. Vogan K (2015) Micropeptide regulates muscle performance. Nat Genet 47(3):198

    CAS  Google Scholar 

  23. Clark N (2018) Small but important. Lab Anim 47(8):207–207

    Google Scholar 

  24. Makarewich CA, Munir AZ, Schiattarella GG, Bezprozvannaya S, Raguimova ON, Cho EE, Vidal AH, Robia SL, Bassel-Duby R, Olson EN (2018) The DWORF micropeptide enhances contractility and prevents heart failure in a mouse model of dilated cardiomyopathy. Elife 7:e38319

    PubMed  PubMed Central  Google Scholar 

  25. Lin Y-F, Xiao M-H, Chen H-X, Meng Y, Zhao N, Yang L, Tang H, Wang J-L, Liu X, Zhu Y (2019) A novel mitochondrial micropeptide MPM enhances mitochondrial respiratory activity and promotes myogenic differentiation. Cell Death Dis 10(7):1–11

    Google Scholar 

  26. Zhu M, Gribskov M (2019) MiPepid: MicroPeptide identification tool using machine learning. BMC Bioinform 20(1):559

    CAS  Google Scholar 

  27. Bi P, McAnally JR, Shelton JM, Sánchez-Ortiz E, Bassel-Duby R, Olson EN (2018) Fusogenic micropeptide Myomixer is essential for satellite cell fusion and muscle regeneration. Proc Natl Acad Sci 115(15):3864–3869

    CAS  PubMed  Google Scholar 

  28. Niu L, Lou F, Sun Y, Sun L, Cai X, Liu Z, Zhou H, Wang H, Wang Z, Bai J, Yin Q, Zhang J, Chen L, Peng D, Xu Z, Gao Y, Tang S, Fan L, Wang H (2020) A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation. Sci Adv 6(21):eaaz2059. https://doi.org/10.1126/sciadv.aaz2059

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Wu S, Zhang L, Deng J, Guo B, Li F, Wang Y, Wu R, Zhang S, Lu J, Zhou Y (2020) A novel micropeptide encoded by Y-linked LINC00278 links cigarette smoking and AR signaling in male esophageal squamous cell carcinoma. Cancer Res. https://doi.org/10.1158/0008-5472.can-19-3440

    Article  PubMed  PubMed Central  Google Scholar 

  30. Li M, Li X, Zhang Y, Wu H, Zhou H, Ding X, Zhang X, Jin X, Wang Y, Yin X, Li C, Yang P, Xu H (2020) Micropeptide MIAC inhibits HNSCC progression by interacting with aquaporin 2. J Am Chem Soc 142(14):6708–6716. https://doi.org/10.1021/jacs.0c00706

    Article  CAS  PubMed  Google Scholar 

  31. Guo B, Wu S, Zhu X, Zhang L, Deng J, Li F, Wang Y, Zhang S, Wu R, Lu J, Zhou Y (2020) Micropeptide CIP2A-BP encoded by LINC00665 inhibits triple-negative breast cancer progression. EMBO J 39(1):e102190. https://doi.org/10.15252/embj.2019102190

    Article  CAS  PubMed  Google Scholar 

  32. Bhatta A, Atianand M, Jiang Z, Crabtree J, Blin J, Fitzgerald KA (2020) A mitochondrial micropeptide is required for activation of the Nlrp3 inflammasome. J Immunol 204(2):428–437. https://doi.org/10.4049/jimmunol.1900791

    Article  CAS  PubMed  Google Scholar 

  33. Ingolia NT, Hussmann JA, Weissman JS (2019) Ribosome profiling: global views of translation. Cold Spring Harbor Perspect Biol 11(5):a032698

    CAS  Google Scholar 

  34. Ingolia NT (2016) Ribosome footprint profiling of translation throughout the genome. Cell 165(1):22–33

    CAS  PubMed  PubMed Central  Google Scholar 

  35. McDermott B, McDonagh B, Clegg P, Tew S (2016) Ribosome profiling: Providing a snapshot of active protein translation by chondrocytic cells in response to interleukin-1β stimulation. Osteoarthritis Cartil 24:S42

    Google Scholar 

  36. Szavits-Nossan J, Ciandrini L (2019) Accurate measures of translation efficiency and traffic using ribosome profiling. BioRxiv 719302. https://doi.org/10.1101/719302

  37. Chen BJ, Byrne FL, Takenaka K, Modesitt SC, Olzomer EM, Mills JD, Farrell R, Hoehn KL, Janitz M (2017) Transcriptome landscape of long intergenic non-coding RNAs in endometrial cancer. Gynecol Oncol 147(3):654–662

    CAS  PubMed  Google Scholar 

  38. Smith JE, Alvarez-Dominguez JR, Kline N, Huynh NJ, Geisler S, Hu W, Coller J, Baker KE (2014) Translation of small open reading frames within unannotated RNA transcripts in Saccharomycescerevisiae. Cell Rep 7(6):1858–1866

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Wyss L, Waser M, Gebetsberger J, Zywicki M, Polacek N (2018) mRNA-specific translation regulation by a ribosome-associated ncRNA in Haloferax volcanii. Sci Rep 8(1):12502

    PubMed  PubMed Central  Google Scholar 

  40. Dominguez E, Zarnowski R, Sanchez H, Covelli A, Westler W, Azadi P, Nett J, Mitchell A, Andes D (2018) Conservation and divergence in the Candida species biofilm matrix mannan-glucan complex structure, function, and genetic control. mBio 9:e00451-18

    PubMed  PubMed Central  Google Scholar 

  41. Chew G-L, Pauli A, Schier AF (2016) Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun 7:11663

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC (2014) Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 33(9):981–993

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Webb TR, Erdmann J, Stirrups KE, Stitziel NO, Masca NG, Jansen H, Kanoni S, Nelson CP, Ferrario PG, König IR (2017) Systematic evaluation of pleiotropy identifies 6 further loci associated with coronary artery disease. J Am Coll Cardiol 69(7):823–836

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Yang M, Lin X, Liu X, Zhang J, Ge F (2018) Genome annotation of a model diatom Phaeodactylumtricornutum using an integrated proteogenomic pipeline. Mol Plant 11(10):1292–1307

    CAS  PubMed  Google Scholar 

  45. Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES (2013) Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154(1):240–251

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Aspden JL, Eyre-Walker YC, Phillips RJ, Amin U, Mumtaz MAS, Brocard M, Couso J-P (2014) Extensive translation of small open reading frames revealed by Poly-Ribo-Seq. Elife 3:e03528

    PubMed  PubMed Central  Google Scholar 

  47. Pueyo JI, Magny EG, Couso JP (2016) New peptides under the s (ORF) ace of the genome. Trends Biochem Sci 41(8):665–678

    CAS  PubMed  Google Scholar 

  48. Verbruggen S, Ndah E, Van Criekinge W, Gessulat S, Kuster B, Wilhelm M, Van Damme P, Menschaert G (2019) PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms. Mol Cell Proteom 18:S126–S140

    CAS  Google Scholar 

  49. Hasbrouck J, Tindal G (2017) An update to compiled ORF norms. Technical Report No. 1702. Online Submission

  50. Olexiouk V, Menschaert G (2019) Using the sORFs. Org database. Org Database Curr Protoc Bioinform 65(1):e68

    Google Scholar 

  51. Wang H, Yang L, Wang Y, Chen L, Li H, Xie Z (2018) RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling. Nucleic Acids Res 47(D1):D230–D234

    PubMed Central  Google Scholar 

  52. Yin X, Jing Y, Xu H (2019) Mining for missed sORF-encoded peptides. Expert Rev Proteom 16(3):257–266

    CAS  Google Scholar 

  53. Leney AC, Heck AJ (2017) Native mass spectrometry: what is in the name? J Am Soc Mass Spectrom 28(1):5–13

    CAS  PubMed  Google Scholar 

  54. Guillarme D, Desfontaine V, Heinisch S, Veuthey J-L (2018) What are the current solutions for interfacing supercritical fluid chromatography and mass spectrometry? J Chromatogr B 1083:160–170

    CAS  Google Scholar 

  55. Smits AH, Vermeulen M (2016) Characterizing protein–protein interactions using mass spectrometry: challenges and opportunities. Trends Biotechnol 34(10):825–834

    CAS  PubMed  Google Scholar 

  56. Rothnagel J, Menschaert G (2018) Short open reading frames and their encoded peptides. Proteomics 18(10):1700035

    Google Scholar 

  57. Yeasmin F, Yada T, Akimitsu N (2018) Micropeptides encoded in transcripts previously identified as long noncoding RNAs: a new chapter in transcriptomics and proteomics. Front Genet 9:144

    PubMed  PubMed Central  Google Scholar 

  58. Fouzia Yeasmin NITT, Kenzui T, Takeshi K, Tetsushi Y, Nobuyoshi A Identification and analysis of short Open Reading Frames (sORFs) on LINC00493 that is initially annotated as noncoding RNAs in human cell. J Biochem. https://doi.org/10.1093/jb/mvaa143

  59. Matsumoto A, Clohessy JG, Pandolfi PP (2017) SPAR, a lncRNA encoded mTORC1 inhibitor. Cell Cycle 16(9):815

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Volders P-J, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P (2014) An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res 43(D1):D174–D180

    PubMed  PubMed Central  Google Scholar 

  61. Verbruggen S (2015) Ribosome profiling, a useful tool in the search for micropeptides. https://lib.ugent.be/catalog/rug01:002216974

  62. Verheggen K, Volders P-J, Mestdagh P, Menschaert G, Van Damme P, Gevaert K, Martens L, Vandesompele J (2017) Noncoding after all: biases in proteomics data do not explain observed absence of lncRNA translation products. J Proteome Res 16(7):2508–2515

    CAS  PubMed  Google Scholar 

  63. Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik Y-K, Van Eyk JE, Liu S, Snyder M, Baker MS (2018) Progress on identifying and characterizing the human proteome: 2018 metrics from the HUPO human proteome project. J Proteome Res 17(12):4031–4041

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Barbieri R, Guryev V, Brandsma CA, Suits F, Bischoff R, Horvatovich P (2016) Proteogenomics: ey driver for clinical discovery and personalized medicine. Adv Exp Med Bio 926:21–47

    CAS  Google Scholar 

  65. Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J (2016) Clinical implications of recent advances in proteogenomics. Expert Re Proteom 13(2):185–199

    CAS  Google Scholar 

  66. Huang T, Bamigbade AT, Xu S, Deng Y, Xie K, Ogunsade OO, Mirza AH, Wang J, Liu P, Zhang S (2020) Identification of a micropeptide on lipid droplet that mediates lipid storage and insulin sensitivity. bioRxiv. https://doi.org/10.1101/2020.04.10.036160

    Article  PubMed  PubMed Central  Google Scholar 

  67. Greninger AL, Knudsen GM, Roychoudhury P, Hanson DJ, Sedlak RH, Xie H, Guan J, Nguyen T, Peddu V, Boeckh M (2018) Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6. BMC Genom 19(1):204

    Google Scholar 

  68. Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J (2017) Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci 114(46):E10018–E10027

    CAS  PubMed  Google Scholar 

  69. Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C (2017) An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Res 27(12):2083–2095

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Low TY, Mohtar MA, Ang MY, Jamal R (2019) Connecting proteomics to next-generation sequencing: proteogenomics and its current applications in biology. Proteomics 19(10):1800235

    Google Scholar 

  71. Hollerer I, Higdon A, Brar GA (2018) Strategies and challenges in identifying function for thousands of sORF-encoded peptides in meiosis. Proteomics 18(10):1700274

    Google Scholar 

  72. Budnik BA, Kellis M, Saghatelian A (2015) Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. J Proteome Res 13(3):1757–1765

    Google Scholar 

  73. Miravet-Verde S, Ferrar T, Espadas-García G, Mazzolini R, Gharrab A, Sabido E, Serrano L, Lluch-Senar M (2019) Unraveling the hidden universe of small proteins in bacterial genomes. Mol Syst Biol 15(2):e8290

    PubMed  PubMed Central  Google Scholar 

  74. Kirk IK, Weinhold N, Brunak S, Belling K (2017) The impact of the protein interactome on the syntenic structure of mammalian genomes. PLoS ONE 12(9):e0179112

    PubMed  PubMed Central  Google Scholar 

  75. Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M (2015) Extensive identification and analysis of conserved small ORFs in animals. Genome Biol 16(1):179

    PubMed  PubMed Central  Google Scholar 

  76. Budamgunta H, Olexiouk V, Luyten W, Schildermans K, Maes E, Boonen K, Menschaert G, Baggerman G (2018) Comprehensive peptide analysis of mouse brain striatum identifies novel sORF-encoded polypeptides. Proteomics 18(10):1700218

    Google Scholar 

  77. Cabrera-Quio LE, Herberg S, Pauli A (2016) Decoding sORF translation–from small proteins to gene regulation. RNA Biol 13(11):1051–1059

    PubMed  PubMed Central  Google Scholar 

  78. Chu Q, Ma J, Saghatelian A (2015) Identification and characterization of sORF-encoded polypeptides. Crit Rev Biochem Mol Biol 50(2):134–141

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Hazarika RR, De Coninck B, Yamamoto LR, Martin LR, Cammue BP, van Noort V (2017) ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsisthaliana. BMC Bioinform 18(1):37

    Google Scholar 

  80. Hazarika RR, De Coninck B, Yamamoto LR, Martin LR, Cammue BP, van Noort V (2017) ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. BMC Bioinform 18(1):37

    Google Scholar 

  81. Surendrarao A (2016) Identifying and understanding processes driving genomic drift of f-box gene families during plant evolution. University of California, Davis

    Google Scholar 

  82. D’Lima NG, Ma J, Winkler L, Chu Q, Loh KH, Corpuz EO, Budnik BA, Lykke-Andersen J, Saghatelian A, Slavoff SA (2017) A human microprotein that interacts with the mRNA decapping complex. Nat Chem Biol 13(2):174

    CAS  PubMed  Google Scholar 

  83. Li L-J, Leng R-X, Fan Y-G, Pan H-F, Ye D-Q (2017) Translation of noncoding RNAs: focus on lncRNAs, pri-miRNAs, and circRNAs. Exp Cell Res 361(1):1–8

    CAS  PubMed  Google Scholar 

  84. Vervliet T, Robinson EL, Roderick HL (2018) Lnc’ing Ca2+, SERCA and cardiac disease. Cell Calcium 72:132–134

    CAS  PubMed  Google Scholar 

  85. Rion N, Rüegg MA (2017) LncRNA-encoded peptides: more than translational noise? Cell Res 27(5):604

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Pauli A, Valen E, Schier AF (2015) Identifying (non-) coding RNAs and small peptides: challenges and opportunities. BioEssays 37(1):103–112

    CAS  PubMed  Google Scholar 

  87. Pauli A, Norris ML, Valen E, Chew G-L, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D (2014) Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 343(6172):1248636

    PubMed  PubMed Central  Google Scholar 

  88. Konina DO, Filatova AY, Skoblov MY (2019) LINC01420 RNA structure and influence on cell physiology. BMC Genom 20(3):298

    Google Scholar 

  89. Robicheau BM, Susko E, Harrigan AM, Snyder M (2017) Ribosomal RNA genes contribute to the formation of pseudogenes and junk DNA in the human genome. Genome Biol Evol 9(2):380–397

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Saghatelian A, Couso JP (2015) Discovery and characterization of smORF-encoded bioactive polypeptides. Nat Chem Biol 11(12):909

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Kaul R, Purushothaman P, Uppal T, Verma SC (2019) KSHV lytic proteins K-RTA and K8 bind to cellular and viral chromatin to modulate gene expression. PLoS ONE 14(4):e0215394

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Tang S, Lomsadze A, Borodovsky M (2015) Identification of protein coding regions in RNA transcripts. Nucleic Acids Res 43(12):e78–e78

    PubMed  PubMed Central  Google Scholar 

  93. Pian C, Zhang G, Chen Z, Chen Y, Zhang J, Yang T, Zhang L (2016) LncRNApred: Classification of long non-coding RNAs and protein-coding transcripts by the ensemble algorithm with a new hybrid feature. PLoS Onse 11(5):e0154567

    Google Scholar 

  94. Combier J-P, Laures-sergues D, Becard G (2017) Use of micropeptides for promoting plant growth (ed). Google Patents

  95. Combier J-P, Laures-sergues D, Becard G (2017) Use of micropeptides in order to stimulate mycorrhizal symbiosis (eds). Google Patents

  96. Wen K, Yang L, Xiong T, Di C, Ma D, Wu M, Xue Z, Zhang X, Long L, Zhang W (2016) Critical roles of long noncoding RNAs in Drosophilaspermatogenesis. Genome Res 26(9):1233–1244

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Zhu M, Hu X, Cao G, Xue R, Gong C (2018) Functions and impact of tal-like genes in animals with regard to applied aspects. Appl Microbiol Biotechnol 102(16):6841–6845

    CAS  PubMed  Google Scholar 

  98. Li K, Tian Y, Yuan Y, Fan X, Yang M, He Z, Yang D (2019) Insights into the functions of LncRNAs in Drosophila. Int J Mol Sci 20(18):4646

    CAS  PubMed Central  Google Scholar 

  99. Tharakan R, Kreimer S, Ubaida-Mohien C, Lavoie J, Olexiouk V, Menschaert G, Ingolia NT, Cole RN, Ishizuka K, Sawa A, Nucifora LG (2020) A methodology for discovering novel brain-relevant peptides: combination of ribosome profiling and peptidomics. Neurosci Res 151:31–37. https://doi.org/10.1016/j.neures.2019.02.006

    Article  CAS  PubMed  Google Scholar 

  100. Kang S, Dahl R, Hsieh W, Shin A, Zsebo KM, Buettner C, Hajjar RJ, Lebeche D (2016) Small molecular allosteric activator of the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) attenuates diabetes and metabolic disorders. J Biol Chem 291(10):5185–5198

    CAS  PubMed  Google Scholar 

  101. Singh DR, Dalton MP, Cho EE, Pribadi MP, Zak TJ, Šeflová J, Makarewich CA, Olson EN, Robia SL (2019) Newly discovered micropeptide regulators of SERCA form oligomers but bind to the pump as monomers. J Mol Biol 431:4429–4443

    CAS  PubMed  PubMed Central  Google Scholar 

  102. Nelson BR, Makarewich CA, Reese AL, Winders BR, Anderson DM, McAnally JR, Kavalali ET, Bassel-Duby R, Olson EN (2015) DWORF: discovery and characterization of a cardiac micropeptide encoded in a putative long noncoding RNA. Circ Res 117(supp_1):A189–A189

    Google Scholar 

  103. Bi P, Ramirez-Martinez A, Li H, Cannavino J, McAnally JR, Shelton JM, Sánchez-Ortiz E, Bassel-Duby R, Olson EN (2017) Control of muscle formation by the fusogenic micropeptide myomixer. Science 356(6335):323–327

    CAS  PubMed  PubMed Central  Google Scholar 

  104. Slavoff SA, Heo J, Budnik BA, Hanakahi LA, Saghatelian A (2014) A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining. J Biol Chem 289(16):10950–10957

    CAS  PubMed  PubMed Central  Google Scholar 

  105. D’Alessandro G, di Fagagna FdA (2018) Long non-coding RNA in the control of genome stability and cancer phenotypes. Non-coding RNA Investig 2(3). https://doi.org/10.21037/ncri.2018.03.01

  106. Hung PJ, Johnson B, Chen B-R, Byrum AK, Bredemeyer AL, Yewdell WT, Johnson TE, Lee BJ, Deivasigamani S, Hindi I (2018) MRI is a DNA damage response adaptor during classical non-homologous end joining. Mol Cell 71(2):332-342.e338

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Xu Z-M, Huang F, Huang W-Q (2018) Angiogenic lncRNAs: a potential therapeutic target for ischaemic heart disease. Life Sci 211:157–171

    CAS  PubMed  Google Scholar 

  108. Frieri M, Kumar K, Boutin A (2017) Antibiotic resistance. J Infect Public Health 10(4):369–378

    PubMed  Google Scholar 

  109. Friedman ND, Temkin E, Carmeli Y (2016) The negative impact of antibiotic resistance. Clin Microbiol Infect 22(5):416–422

    CAS  PubMed  Google Scholar 

  110. Wang J, Chou S, Yang Z, Yang Y, Wang Z, Song J, Dou X, Shan A (2018) Combating drug-resistant fungi with novel imperfectly amphipathic palindromic peptides. J Med Chem 61(9):3889–3907

    CAS  PubMed  Google Scholar 

  111. Trepos R, Cervin G, Pile C, Pavia H, Hellio C, Svenson J (2015) Evaluation of cationic micropeptides derived from the innate immune system as inhibitors of marine biofouling. Biofouling 31(4):393–403

    CAS  PubMed  Google Scholar 

  112. Starr CG, He J, Wimley WC (2016) Host cell interactions are a significant barrier to the clinical utility of peptide antibiotics. ACS Chem Biol 11(12):3391–3399

    CAS  PubMed  PubMed Central  Google Scholar 

  113. Sánchez-Gómez S, Ferrer-Espada R, Stewart PS, Pitts B, Lohner K, de Tejada GM (2015) Antimicrobial activity of synthetic cationic peptides and lipopeptides derived from human lactoferricin against Pseudomonasaeruginosa planktonic cultures and biofilms. BMC Microbiol 15(1):137

    PubMed  PubMed Central  Google Scholar 

  114. Tabish Rehman M, U Khan A (2015) Understanding the interaction between human serum albumin and anti-bacterial/anti-cancer compounds. Curr Pharm Des 21(14):1785–1799

    Google Scholar 

  115. Svendsen JSM, Grant TM, Rennison D, Brimble MA, Svenson J (2019) Very short and stable lactoferricin-derived antimicrobial peptides: design principles and potential uses. Acc Chem Res 52(3):749–759

    CAS  PubMed  Google Scholar 

  116. Le L, Bokare A, Erogbogbo F (2018) Hand powered, cost effective, 3D printed nanoparticle synthesizer: effects of polymer end caps, drugs, and solvents on lipid polymer hybrid nanoparticles. Mater Res Express 6(2):025403

    Google Scholar 

  117. Lee J, Lee DG (2015) Antimicrobial peptides (AMPs) with dual mechanisms: membrane disruption and apoptosis. J Microbiol Biotechnol 25(6):759–764

    CAS  PubMed  Google Scholar 

  118. Sim J-Y, Kim S, Lee J, Lim H, Kim HH, Park Z-Y, Kim JI (2019) A significantly enhanced antibacterial spectrum of D-enantiomeric lipopeptide bactenecin. Biochem Biophys Res Commun 514(2):497–502

    CAS  PubMed  Google Scholar 

  119. Pang W, Lv J, Du S, Wang J, Wang J, Zeng Y (2017) Preparation of curcumin-piperazine coamorphous phase and fluorescence spectroscopic and density functional theory simulation studies on the interaction with bovine serum albumin. Mol Pharm 14(9):3013–3024

    CAS  PubMed  Google Scholar 

  120. De Freitas GB, De Almeida DJ, Carraro E, Kerppers II, Martins GA, Mainardes RM, Khalil NM, Messias-Reason IJ (2018) Formulation, characterization, and in vitro/in vivo studies of capsaicin-loaded albumin nanoparticles. Mater Sci Eng C 93:70–79

    Google Scholar 

  121. Bolattin MB, Nandibewoor ST, Joshi SD, Dixit SR, Chimatadar SA (2016) Interaction between carisoprodol and bovine serum albumin and effect of β-cyclodextrin on binding: insights from molecular docking and spectroscopic techniques. RSC Adv 6(68):63463–63471

    CAS  Google Scholar 

  122. Tsai C-Y, Chen Y-J, Fu Y-S, Chang L-S (2015) Antibacterial and membrane-damaging activities of mannosylated bovine serum albumin. Arch Biochem Biophys 573:14–22

    CAS  PubMed  Google Scholar 

  123. Iavarone F, Desiderio C, Vitali A, Messana I, Martelli C, Castagnola M, Cabras T (2018) Cryptides: latent peptides everywhere. Crit Rev Biochem Mol Biol 53(3):246–263

    CAS  PubMed  Google Scholar 

  124. Li W, Cui T, Hu L, Wang Z, Li Z, He Z-G (2015) Cyclic diguanylate monophosphate directly binds to human siderocalin and inhibits its antibacterial activity. Nat Commun 6:8330

    CAS  PubMed  PubMed Central  Google Scholar 

  125. Rogoyski OM, Pueyo JI, Couso JP, Newbury SF (2017) Functions of long non-coding RNAs in human disease and their conservation in Drosophila development. Biochem Soc Trans 45(4):895–904

    CAS  PubMed  Google Scholar 

  126. Haemmig S, Feinberg M (2018) Manipulation of long non-coding RNAs in cardiovascular disease using genome editing technology. In: Church G, Appasani K (ed) Genome editing and engineering: from TALENs, ZFNs and CRISPRs to molecular surgery. Cambridge University Press, Cambridge, pp 371–388. https://doi.org/10.1017/9781316756300.026

    Chapter  Google Scholar 

  127. Kato-Inui T, Takahashi G, Hsu S, Miyaoka Y (2018) Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair. Nucleic Acids Res 46(9):4677–4688

    CAS  PubMed  PubMed Central  Google Scholar 

  128. Goff LA, Rinn JL (2015) Linking RNA biology to lncRNAs. Genome Res 25(10):1456–1465

    CAS  PubMed  PubMed Central  Google Scholar 

  129. Olson E, Millay DP (2019) Compositions and methods relating to myomaker-induced muscle cell fusion (eds). Google Patents

  130. Mallory AC, Shkumatava A (2015) LncRNAs in vertebrates: advances and challenges. Biochimie 117:3–14

    CAS  PubMed  PubMed Central  Google Scholar 

  131. Linse KD, Castro J What are micro peptides? https://blog-biosyn.com/2013/05/07/what-are-micro-peptides/

  132. Ransohoff JD, Wei Y, Khavari PA (2018) The functions and unique features of long intergenic non-coding RNA. Nat Rev Mol Cell Biol 19(3):143

    CAS  PubMed  Google Scholar 

  133. Pymm P, Illing PT, Ramarathinam SH, O’Connor GM, Hughes VA, Hitchen C, Price DA, Ho BK, McVicar DW, Brooks AG (2017) MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape. Nat Struct Mol Biol 24(4):387

    CAS  PubMed  PubMed Central  Google Scholar 

  134. Satpathy AT, Chang HY (2015) Long noncoding RNA in hematopoiesis and immunity. Immunity 42(5):792–804

    CAS  PubMed  Google Scholar 

  135. Ray S, Rosenberg MI, Chanut-Delalande H, Decaras A, Schwertner B, Toubiana W, Auman T, Schnellhammer I, Teuscher M, Khila A (2018) Millepattes micropeptides are an ancient developmental switch required for embryonic patterning. BioRxiv 376111. https://doi.org/10.1101/376111

  136. Zhan R, Li X, Guo W, Liu X, Liu Z, Xu K, Tang B (2019) An Aptamer-based near-infrared fluorescence nanoprobe for detecting and imaging of phospholamban micropeptide in cardiomyocytes. ACS Sens 4(3):733–739

    CAS  PubMed  Google Scholar 

  137. Zhang J, Naik HS, Assefa T, Sarkar S, Reddy RC, Singh A, Ganapathysubramanian B, Singh AK (2017) Computer vision and machine learning for robust phenotyping in genome-wide studies. Sci Rep 7:44048

    PubMed  PubMed Central  Google Scholar 

  138. Sahu B, Pani S, Swalsingh G, Bal NC (2019) Epigenetic mechanisms in regulation of adaptive thermogenesis in skeletal muscle. Front Endocrinol 10:517

    Google Scholar 

  139. Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DY, Seydoux G, Mohr SE, Zuber J, Perrimon N (2017) Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet 18(1):24

    CAS  PubMed  Google Scholar 

  140. Gilmore C, Somasundaram V, Scheiblin D, Heinz W, Lockett S, Wink D (2019) Restricting diffusive exchange in vitro demonstrates inos modulates hypoxic gradients in the tumor microenvironment. Biophys J 116(3):284a

    Google Scholar 

  141. Niu Z, Zhang W, Yu C, Zhang J, Wen Y (2018) Recent advances in biological sample preparation methods coupled with chromatography, spectrometry and electrochemistry analysis techniques. TrAC Trends Anal Chem 102:123–146

    CAS  Google Scholar 

  142. Li L, Andrén PE, Sweedler JV (2018) Editorial and review: 29th ASMS sanibel conference on mass spectrometry—peptidomics: bridging the gap between proteomics and metabolomics by MS. J Am Soc Mass Spectrom 29(5):801–806

    CAS  PubMed  Google Scholar 

  143. Fricker L (2018) Quantitative peptidomics: general considerations. Methods Mol Biol 1719:121–140. https://doi.org/10.1007/978-1-4939-7537-2_8

    Article  CAS  PubMed  Google Scholar 

  144. Zhang H, Ji X, Li P, Liu C, Lou J, Wang Z, Wen W, Xiao Y, Zhang M, Zhu X (2020) Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci China Life Sci 63(7):953–985. https://doi.org/10.1007/s11427-020-1702-x

    Article  PubMed  Google Scholar 

  145. Alberti S, Gladfelter A, Mittag T (2019) Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell 176(3):419–434. https://doi.org/10.1016/j.cell.2018.12.035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD, Baldwin AJ (2015) Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 57(5):936–947. https://doi.org/10.1016/j.molcel.2015.01.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Wang J, Choi J-M, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D, Poser I, Pappu RV, Alberti S, Hyman AA (2018) A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174(3):688-699.e616. https://doi.org/10.1016/j.cell.2018.06.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Dasgupta S, Yang C, Castro LM, Tashima AK, Ferro ES, Moir RD, Willis IM, Fricker LD (2016) Analysis of the yeast peptidome and comparison with the human peptidome. PLoS ONE 11(9):e0163312

    PubMed  PubMed Central  Google Scholar 

  149. Zelanis A, Silva DA, Kitano ES, Liberato T, Fukushima I, Serrano SM, Tashima AK (2019) A first step towards building spectral libraries as complementary tools for snake venom proteome/peptidome studies. Comp Biochem Physiol Part D Genom Proteom 31:100599

    CAS  Google Scholar 

  150. Liu T, Rodland KD, Smith RD (2018) Characterization of the ovarian tumor peptidome. Vitam Horm 107:515–531. https://doi.org/10.1016/bs.vh.2018.01.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Piovesana S, Capriotti AL, Cavaliere C, La Barbera G, Samperi R, Chiozzi RZ, Laganà A (2015) Peptidome characterization and bioactivity analysis of donkey milk. J Proteom 119:21–29

    CAS  Google Scholar 

  152. Cao H, Shao F, Li M, Sweat M, Qian Q, Guo Y, Amendt B, Yang L (2019) Comprehensive identification of micropeptides encoded by long noncoding RNAs in human tissues. FASEB J 33(1_supplement):714.711-714.711

    Google Scholar 

  153. Skarshewski A, Stanton-Cook M, Huber T, Al Mansoori S, Smith R, Beatson SA, Rothnagel JA (2014) uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation. BMC Bioinform 15:36. https://doi.org/10.1186/1471-2105-15-36

    Article  CAS  Google Scholar 

  154. Lin MF, Jungreis I, Kellis M (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics (Oxf Engl) 27(13):i275–i282. https://doi.org/10.1093/bioinformatics/btr209

    Article  CAS  Google Scholar 

  155. Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH (2010) sORF finder: a program package to identify small open reading frames with high coding potential. Bioinformatics (Oxf Engl) 26(3):399–400. https://doi.org/10.1093/bioinformatics/btp688

    Article  CAS  Google Scholar 

  156. Casimiro-Soriguer CS, Rigual MM, Brokate-Llanos AM, Muñoz MJ, Garzón A, Pérez-Pulido AJ, Jimenez J (2020) Using AnABlast for intergenic sORF prediction in the C.elegans genome. Bioinformatics (Oxf Engl). https://doi.org/10.1093/bioinformatics/btaa608

    Article  Google Scholar 

  157. Hu L, Xu Z, Hu B, Lu ZJ (2017) COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features. Nucleic Acids Res 45(1):e2–e2. https://doi.org/10.1093/nar/gkw798

    Article  CAS  PubMed  Google Scholar 

  158. Crappé J, Van Criekinge W, Trooskens G, Hayakawa E, Luyten W, Baggerman G, Menschaert G (2013) Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs. BMC Genom 14(1):648. https://doi.org/10.1186/1471-2164-14-648

    Article  CAS  Google Scholar 

  159. Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147(4):789–802. https://doi.org/10.1016/j.cell.2011.10.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15(3):205–213. https://doi.org/10.1038/nrg3645

    Article  CAS  PubMed  Google Scholar 

  161. Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS (2015) A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation. Mol Cell 60(5):816–827. https://doi.org/10.1016/j.molcel.2015.11.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U (2016) Detecting actively translated open reading frames in ribosome profiling data. Nat Methods 13(2):165–170. https://doi.org/10.1038/nmeth.3688

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors thank the Portuguese Foundation for Science and Technology (FCT), European Union, QREN, FEDER and COMPETE for funding UnIC—Unidade de Investigação Cardiovascular (UIDB/00051/2020 and UIDP/00051/2020), iBiMED (UIDB/04501/2020, POCI-01-0145-FEDER-007628), LAQV/REQUIMTE (UIDB/50006/2020) research units. RV is supported by IF/00286/2015 grants.

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Vitorino, R., Guedes, S., Amado, F. et al. The role of micropeptides in biology. Cell. Mol. Life Sci. 78, 3285–3298 (2021). https://doi.org/10.1007/s00018-020-03740-3

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