Abstract: With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides (miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function. MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.

微肽：起源、鉴定及其在代谢相关疾病中的作用

[1]AdamsBD, ParsonsC, WalkerL, et al., 2017. Targeting noncoding RNAs in disease. J Clin Invest, 127(3):761-771.

[2]AkimotoC, SakashitaE, KasashimaK, et al., 2013. Translational repression of the McKusick-Kaufman syndrome transcript by unique upstream open reading frames encoding mitochondrial proteins with alternative polyadenylation sites. Biochim Biophys Acta, 1830(3):2728-2738.

[3]AndersonDM, AndersonKM, ChangCL, et al., 2015. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell, 160(4):595-606.

[4]AndjusS, MorillonA, WeryM, 2021. From yeast to mammals, the nonsense-mediated mRNA decay as a master regulator of long non-coding RNAs functional trajectory. Non-Coding RNA, 7(3):44.

[5]AspdenJL, Eyre-WalkerYC, PhillipsRJ, et al., 2014. Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. Elife, 3:e03528.

[6]BalNC, MauryaSK, SopariwalaDH, et al., 2012. Sarcolipin is a newly identified regulator of muscle-based thermogenesis in mammals. Nat Med, 18(10):1575-1579.

[7]BazziniAA, JohnstoneTG, ChristianoR, et al., 2014. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J, 33(9):981-993.

[8]BhatiKK, BlaakmeerA, ParedesEB, et al., 2018. Approaches to identify and characterize microproteins and their potential uses in biotechnology. Cell Mol Life Sci, 75(14):2529-2536.

[9]BhattaA, AtianandM, JiangZZ, et al., 2020. A mitochondrial micropeptide is required for activation of the Nlrp3 inflammasome. J Immunol, 204(2):428-437.

[10]BoguszewskaK, SzewczukM, Kaźmierczak-BarańskaJ, et al., 2020. The similarities between human mitochondria and bacteria in the context of structure, genome, and base excision repair system. Molecules, 25(12):2857.

[11]BrancaRMM, OrreLM, JohanssonHJ, et al., 2014. HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat Methods, 11(1):59-62.

[12]CaoXW, KhitunA, NaZ, et al., 2020. Comparative proteomic profiling of unannotated microproteins and alternative proteins in human cell lines. J Proteome Res, 19(8):‍3418-3426.

[13]CataldoLR, Fernández-VerdejoR, SantosJL, et al., 2018. Plasma MOTS-c levels are associated with insulin sensitivity in lean but not in obese individuals. J Investig Med, 66(6):1019-1022.

[14]ChenJ, BrunnerAD, CoganJZ, et al., 2020. Pervasive functional translation of noncanonical human open reading frames. Science, 367(6482):1140-1146.

[15]ChenXP, HanP, ZhouT, et al., 2016. CircRNADb: a comprehensive database for human circular RNAs with protein-coding annotations. Sci Rep, 6:34985.

[16]ChenY, HoL, TergaonkarV, 2021. sORF-Encoded MicroPeptides: new players in inflammation, metabolism, and precision medicine. Cancer Lett, 500:263-270.

[17]ChngSC, HoL, TianJ, et al., 2013. ELABELA: a hormone essential for heart development signals via the apelin receptor. Dev Cell, 27(6):672-680.

[18]ChothaniSP, AdamiE, WidjajaAA, et al., 2022. A high-resolution map of human RNA translation. Mol Cell, 82(15):2885-2899.e8.

[19]ChugunovaA, LosevaE, MazinP, et al., 2019. LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism. Proc Natl Acad Sci USA, 116(11):4940-4945.

[20]CobbLJ, LeeC, XiaoJL, et al., 2016. Naturally occurring mitochondrial-derived peptides are age-dependent regulators of apoptosis, insulin sensitivity, and inflammatory markers. Aging, 8(4):796-809.

[21]DangelmaierEA, LiXL, HartfordCCR, et al., 2022. An evolutionarily conserved AU-rich element in the 3' untranslated region of a transcript misannotated as a long noncoding RNA regulates RNA stability. Mol Cell Biol, 42(4):e00505-21.

[22]DragomirMP, ManyamGC, OttLF, et al., 2020. FuncPEP: a database of functional peptides encoded by non-coding RNAs. Non-Coding RNA, 6(4):41.

[23]DuCQ, ZhangC, WuW, et al., 2018. Circulating MOTS-c levels are decreased in obese male children and adolescents and associated with insulin resistance. Pediatr Diabetes, 19(6):1058-1064.

[24]The ENCODE Project Consortium, 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146):799-816.

[25]FabreB, CombierJP, PlazaS, 2021. Recent advances in mass spectrometry-based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions. Curr Opin Chem Biol, 60:122-130.

[26]FerenceBA, GinsbergHN, GrahamI, et al., 2017. Low-density lipoproteins cause atherosclerotic cardiovascular disease. 1. Evidence from genetic, epidemiologic, and clinical studies. A consensus statement from the European Atherosclerosis Society Consensus Panel. Eur Heart J, 38(32):‍2459-2472.

[27]FriesenM, WarrenCR, YuHJ, et al., 2020. Mitoregulin controls β‍-oxidation in human and mouse adipocytes. Stem Cell Rep, 14(4):590-602.

[28]FungG, ShiJ, DengH, et al., 2015. Cytoplasmic translocation, aggregation, and cleavage of TDP-43 by enteroviral proteases modulate viral pathogenesis. Cell Death Differ, 22(12):2087-2097.

[29]GammagePA, MoraesCT, MinczukM, 2018. Mitochondrial genome engineering: the revolution may not be CRISPR-ized. Trends Genet, 34(2):101-110.

[30]GeQW, JiaDJC, CenD, et al., 2021. Micropeptide ASAP encoded by LINC00467 promotes colorectal cancer progression by directly modulating ATP synthase activity. J Clin Invest, 131(22):e152911.

[31]GuoBB, WuSQ, ZhuX, et al., 2020. Micropeptide CIP2A-BP encoded by LINC00665 inhibits triple-negative breast cancer progression. EMBO J, 39(1):e102190.

[32]GustafssonCM, FalkenbergM, LarssonNG, 2016. Maintenance and expression of mammalian mitochondrial DNA. Annu Rev Biochem, 85:133-160.

[33]HartfordCCR, LalA, 2020. When long noncoding becomes protein coding. Mol Cell Biol, 40(6):e00528-19.

[34]HashimotoY, NiikuraT, TajimaH, et al., 2001. A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer’s disease genes and Aβ. Proc Natl Acad Sci USA, 98(11):6336-6341.

[35]HuangJZ, ChenM, ChenD, et al., 2017. A peptide encoded by a putative lncRNA HOXB-AS3 suppresses colon cancer growth. Mol Cell, 68(1):171-184.e6.

[36]HussainSRA, YalvacME, KhooB, et al., 2021. Adapting CRISPR/Cas9 system for targeting mitochondrial genome. Front Genet, 12:627050.

[37]IngoliaNT, GhaemmaghamiS, NewmanJRS, et al., 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324(5924):218-223.

[38]IngoliaNT, BrarGA, Stern-GinossarN, et al., 2014. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep, 8(5):1365-1379.

[39]JiZ, SongRS, RegevA, et al., 2015. Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins. Elife, 4:e08890.

[40]JohnstoneTG, BazziniAA, GiraldezAJ, 2016. Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J, 35(7):706-723.

[41]KampsR, SzklarczykR, TheunissenTE, et al., 2018. Genetic defects in mtDNA-encoded protein translation cause pediatric, mitochondrial cardiomyopathy with early-onset brain disease. Eur J Hum Genet, 26(4):537-551.

[42]KangM, TangB, LiJX, et al., 2020. Identification of miPEP133 as a novel tumor-suppressor microprotein encoded by miR-34a pri-miRNA. Mol Cancer, 19:143.

[43]KapustaA, KronenbergZ, LynchVJ, et al., 2013. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet, 9(4):e1003470.

[44]KearseMG, WiluszJE, 2017. Non-AUG translation: a new start for protein synthesis in eukaryotes. Genes Dev, 31(17):1717-1731.

[45]KhitunA, SlavoffSA, 2019. Proteomic detection and validation of translated small open reading frames. Curr Protoc Chem Biol, 11(4):e77.

[46]KhitunA, NessTJ, SlavoffSA, 2019. Small open reading frames and cellular stress responses. Mol Omics, 15(2):108-116.

[47]KuliawatR, KleinL, GongZW, et al., 2013. Potent humanin analog increases glucose-stimulated insulin secretion through enhanced metabolism in the β cell. FASEB J, 27(12):4890-4898.

[48]KustatscherG, GrabowskiP, SchraderTA, et al., 2019. Co-regulation map of the human proteome enables identification of protein functions. Nat Biotechnol, 37(11):‍1361-1371.

[49]KuwaharaK, 2021. The natriuretic peptide system in heart failure: diagnostic and therapeutic implications. Pharmacol Ther, 227:107863.

[50]LauresserguesD, CouzigouJM, ClementeHS, et al., 2015. Primary transcripts of microRNAs encode regulatory peptides. Nature, 520(7545):90-93.

[51]LeeC, ZengJ, DrewBG, et al., 2015. The mitochondrial-derived peptide MOTS-c promotes metabolic homeostasis and reduces obesity and insulin resistance. Cell Metab, 21(3):443-454.

[52]LiQY, LuHY, HuGY, et al., 2019. Earlier changes in mice after D-galactose treatment were improved by mitochondria derived small peptide MOTS-c. Biochem Biophys Res Commun, 513(2):439-445.

[53]LiangS, BellatoHM, LorentJ, et al., 2018. Polysome-profiling in small tissue samples. Nucleic Acids Res, 46(1):e3.

[54]LuHY, WeiM, ZhaiY, et al., 2019. MOTS-c peptide regulates adipose homeostasis to prevent ovariectomy-induced metabolic dysfunction. J Mol Med, 97(4):473-485.

[55]LubecG, Afjehi-SadatL, 2007. Limitations and pitfalls in protein identification by mass spectrometry. Chem Rev, 107(8):3568-3584.

[56]MaJ, DiedrichJK, JungreisI, et al., 2016. Improved identification and analysis of small open reading frame encoded polypeptides. Anal Chem, 88(7):3967-3975.

[57]MaZ, SongJJ, MartinS, et al., 2021. The Elabela-APJ axis: a promising therapeutic target for heart failure. Heart Fail Rev, 26(5):1249-1258.

[58]MackowiakSD, ZauberH, BielowC, et al., 2015. Extensive identification and analysis of conserved small ORFs in animals. Genome Biol, 16:179.

[59]MagnyEG, PueyoJI, PearlFMG, et al., 2013. Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames. Science, 341(6150):1116-1120.

[60]MakarewichCA, OlsonEN, 2017. Mining for micropeptides. Trends Cell Biol, 27(9):685-696.

[61]MakarewichCA, BaskinKK, MunirAZ, et al., 2018. MOXI is a mitochondrial micropeptide that enhances fatty acid β-oxidation. Cell Rep, 23(13):3701-3709.

[62]MakarewichCA, MunirAZ, BezprozvannayaS, et al., 2022. The cardiac-enriched microprotein mitolamban regulates mitochondrial respiratory complex assembly and function in mice. Proc Natl Acad Sci USA, 119(6):e2120476119.

[63]MasvidalL, HuleaL, FuricL, et al., 2017. mTOR-sensitive translation: cleared fog reveals more trees. RNA Biol, 14(10):1299-1305.

[64]MatsumotoA, PasutA, MatsumotoM, et al., 2017. mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide. Nature, 541(7636):228-232.

[65]MerryTL, ChanA, WoodheadJST, et al., 2020. Mitochondrial-derived peptides in energy metabolism. Am J Physiol Endocrinol Metab, 319(4):E659-E666.

[66]MillerB, KimSJ, KumagaiH, et al., 2022a. Mitochondria-derived peptides in aging and healthspan. J Clin Invest, 132(9):e158449.

[67]MillerB, KimSJ, MehtaHH, et al., 2022b. Mitochondrial DNA variation in Alzheimer’s disease reveals a unique microprotein called SHMOOSE. Mol Psychiatry, 28(4):1813-1826.

[68]MuzumdarRH, HuffmanDM, AtzmonG, et al., 2009. Humanin: a novel central regulator of peripheral insulin action. PLoS ONE, 4(7):e6334.

[69]NishikimiT, NakagawaY, MinaminoN, et al., 2015. Pro-B-type natriuretic peptide is cleaved intracellularly: impact of distance between O-glycosylation and cleavage sites. Am J Physiol Regul Integr Comp Physiol, 309(6):R639-R649.

[70]NiuLM, LouFZ, SunY, et al., 2020. A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation. Sci Adv, 6(21):eaaz2059.

[71]OuspenskaiaT, LawT, ClauserKR, et al., 2022. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol, 40(2):209-217.

[72]PanJF, WangRJ, ShangFZ, et al., 2022. Functional micropeptides encoded by long non-coding RNAs: a comprehensive review. Front Mol Biosci, 9:817517.

[73]PatraquimP, MumtazMAS, PueyoJI, et al., 2020. Developmental regulation of canonical and small ORF translation from mRNAs. Genome Biol, 21:128.

[74]PauliA, NorrisML, ValenE, et al., 2014. Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science, 343(6172):1248636.

[75]PolenkowskiM, Burbano de LaraS, AllisterAB, et al., 2021. Identification of novel micropeptides derived from hepatocellular carcinoma-specific long noncoding RNA. Int J Mol Sci, 23(1):58.

[76]PotenzaMA, SgarraL, DesantisV, et al., 2021. Diabetes and Alzheimer’s disease: might mitochondrial dysfunction help deciphering the common path? Antioxidants, 10(8):1257.

[77]PratsAC, DavidF, DialloLH, et al., 2020. Circular RNA, the key for translation. Int J Mol Sci, 21(22):8591.

[78]PrimeauJO, ArmaniousGP, FisherME, et al., 2018. The SarcoEndoplasmic reticulum calcium ATPase. In: Harris JR, Boekema EJ (Eds.), Membrane Protein Complexes: Structure and Function. Springer, Singapore, p.229-258.

[79]QuL, HeXY, TangQ, et al., 2022. Iron metabolism, ferroptosis, and lncRNA in cancer: knowns and unknowns. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 23(10):844-862.

[80]RamzyA, KiefferTJ, 2022. Altered islet prohormone processing: a cause or consequence of diabetes? Physiol Rev, 102(1):155-208.

[81]RanFA, HsuPD, WrightJ, et al., 2013. Genome engineering using the CRISPR-Cas9 system. Nat Protoc, 8(11):2281-2308.

[82]RathoreA, ChuQ, TanD, et al., 2018. MIEF1 microprotein regulates mitochondrial translation. Biochemistry, 57(38):5564-5575.

[83]RinnJL, ChangHY, 2012. Genome regulation by long noncoding RNAs. Annu Rev Biochem, 81:145-166.

[84]RothzergE, XuJK, WoodD, 2022. Identification of differentially expressed intronic transcripts in osteosarcoma. Non-Coding RNA, 8(6):73.

[85]Ruiz-OreraJ, AlbàMM, 2019. Translation of small open reading frames: roles in regulation and evolutionary innovation. Trends Genet, 35(3):186-198.

[86]SatoT, SatoC, KadowakiA, et al., 2017. ELABELA-APJ axis protects from pressure overload heart failure and angiotensin II-induced cardiac damage. Cardiovasc Res, 113(7):760-769.

[87]SchindewolfC, BraunS, DomdeyH, 1996. In vitro generation of a circular exon from a linear pre-mRNA transcript. Nucleic Acids Res, 24(7):1260-1266.

[88]SinhaT, PanigrahiC, DasD, et al., 2022. Circular RNA translation, a path to hidden proteome. Wiley Interdiscip Rev RNA, 13(1):e1685.

[89]StarckSR, TsaiJC, ChenKL, et al., 2016. Translation from the 5' untranslated region shapes the integrated stress response. Science, 351(6272):aad3867.

[90]StaudtAC, WenkelS, 2011. Regulation of protein function by ‘microProteins’. EMBO Rep, 12(1):35-42.

[91]SteinCS, JadiyaP, ZhangXM, et al., 2018. Mitoregulin: a lncRNA-encoded microprotein that supports mitochondrial supercomplexes and respiratory efficiency. Cell Rep, 23(13):3710-3720.e8.

[92]TezzeC, RomanelloV, DesbatsMA, et al., 2017. Age-associated loss of OPA1 in muscle impacts muscle mass, metabolic homeostasis, systemic inflammation, and epithelial senescence. Cell Metab, 25(6):1374-1389.e6.

[93]TharakanR, SawaA, 2021. Minireview: novel micropeptide discovery by proteomics and deep sequencing methods. Front Genet, 12:651485.

[94]TumminiaA, VinciguerraF, ParisiM, et al., 2018. Type 2 diabetes mellitus and Alzheimer’s disease: role of insulin signalling and therapeutic implications. Int J Mol Sci, 19(11):3306.

[95]UlitskyI, BartelDP, 2013. lincRNAs: genomics, evolution, and mechanisms. Cell, 154(1):26-46.

[96]van HeeschS, WitteF, Schneider-LunitzV, et al., 2019. The translational landscape of the human heart. Cell, 178(1):242-260.e29.

[97]VitorinoR, GuedesS, AmadoF, et al., 2021. The role of micropeptides in biology. Cell Mol Life Sci, 78(7):3285-3298.

[98]VizioliMG, LiuTH, MillerKN, et al., 2020. Mitochondria-to-nucleus retrograde signaling drives formation of cytoplasmic chromatin and inflammation in senescence. Genes Dev, 34(5-6):428-445.

[99]WaiT, García-PrietoJ, BakerMJ, et al., 2015. Imbalanced OPA1 processing and mitochondrial fragmentation cause heart failure in mice. Science, 350(6265):aad0116.

[100]WangJZ, ZhuS, MengN, et al., 2019. ncRNA-encoded peptides or proteins and cancer. Mol Ther, 27(10):1718-1725.

[101]WangS, MaoCB, LiuSR, 2019. Peptides encoded by noncoding genes: challenges and perspectives. Signal Transduct Target Ther, 4:57.

[102]WilsonBA, MaselJ, 2011. Putatively noncoding transcripts show extensive association with ribosomes. Genome Biol Evol, 3:1245-1252.

[103]WinterJ, JungS, KellerS, et al., 2009. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol, 11(3):228-234.

[104]WongJ, ZhangJC, YanagawaB, et al., 2012. Cleavage of serum response factor mediated by enteroviral protease 2A contributes to impaired cardiac function. Cell Res, 22(2):360-371.

[105]WuWY, JiPF, ZhaoFQ, 2020. CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Genome Biol, 21:101.

[106]WuY, SunLK, ZhuangZD, et al., 2022. Mitochondrial-derived peptides in diabetes and its complications. Front Endocrinol, 12:808120.

[107]XuK, JinXY, LuoY, et al., 2023. Spatial transcriptome analysis of long non-coding RNAs reveals tissue specificity and functional roles in cancer. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 24(1):15-31.

[108]XuYT, ZhangL, OcanseyDKW, et al., 2022. HucMSC-Ex alleviates inflammatory bowel disease via the lnc78583-mediated miR3202/HOXB13 pathway. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 23(5):423-431.

[109]YangJE, ZhongWJ, LiJF, et al., 2023. LINC00998-encoded micropeptide SMIM30 promotes the G1/S transition of cell cycle by regulating cytosolic calcium level. Mol Oncol, 17(5):901-916.

[110]YangYB, GaoXY, ZhangML, et al., 2018. Novel role of FBXW7 circular RNA in repressing glioma tumorigenesis. J Natl Cancer Inst, 110(3):304-315.

[111]YaoJ, IrwinRW, ZhaoLQ, et al., 2009. Mitochondrial bioenergetic deficit precedes Alzheimer’s pathology in female mouse model of Alzheimer’s disease. Proc Natl Acad Sci USA, 106(34):14670-14675.

[112]ZárateSC, TraettaME, CodagnoneMG, et al., 2019. Humanin, a mitochondrial-derived peptide released by astrocytes, prevents synapse loss in hippocampal neurons. Front Aging Neurosci, 11:123.

[113]ZhangS, ReljićB, LiangC, et al., 2020. Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly. Nat Commun, 11:1312.

[114]ZhangY, HuangNQ, YanF, et al., 2018. Diabetes mellitus and Alzheimer’s disease: GSK-3β as a potential link. Behav Brain Res, 339:57-65.

[115]ZhuLF, XuL, WangCG, et al., 2021. T6SS translocates a micropeptide to suppress STING-mediated innate immunity by sequestering manganese. Proc Natl Acad Sci USA, 118(42):e2103526118.