1
|
Agrawal A, Saghatelian A. Identification of microproteins with transactivation activity by polyalanine motif selection. RSC Chem Biol 2025; 6:800-808. [PMID: 40083654 PMCID: PMC11898273 DOI: 10.1039/d4cb00277f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Accepted: 02/26/2025] [Indexed: 03/16/2025] Open
Abstract
Microproteins are an emerging class of proteins that are encoded by small open reading frames (smORFs) less than or equal to 100 amino acids. The functions of several microproteins have been illuminated through phenotypic screening or protein-protein interaction studies, but thousands of microproteins remain uncharacterized. The functional characterization of microproteins is challenging due to a lack of sequence homology. Here, we demonstrate a strategy to enrich microproteins that contain specific motifs as a means to more rapidly characterize microproteins. Specifically, we used the fact that polyalanine motifs are associated with nuclear proteins to select 58 candidate microproteins to screen for transactivation function. We identified three microproteins with transactivation activity when tested as GAL4-fusions in a cell-based luciferase assay. The results support the continued use of the motif selection strategy for the discovery of microprotein function.
Collapse
Affiliation(s)
- Archita Agrawal
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies La Jolla CA USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies La Jolla CA USA
| |
Collapse
|
2
|
Otsune S, Matsuka M, Shirakashi C, Zhang X, Nakagoshi H. Polished Rice Regulates Maturation but Not Survival of Secondary Cells in Drosophila Male Accessory Gland. Genes Cells 2025; 30:e70025. [PMID: 40346918 PMCID: PMC12065019 DOI: 10.1111/gtc.70025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2025] [Revised: 04/14/2025] [Accepted: 04/29/2025] [Indexed: 05/12/2025]
Abstract
In Drosophila males, the accessory gland is responsive to nutrient signal-dependent regulation of fertility/fecundity. The accessory gland is composed of two types of binucleated epithelial cells, about 1000 main cells and 60 secondary cells (SCs). The transcription factors Defective proventriculus (Dve), Abdominal-B, and Ecdysone receptors (EcRs) are strongly expressed in adult SCs. In response to nutrient conditions during development, coordinated action between Dve and ecdysone signaling determines the optimal number of SCs and regulates their maturation. A downstream effector of ecdysone signaling, Ftz-F1, is crucial in this process. Another downstream effector, Polished rice (Pri), is small peptides of 11 or 32 amino acids. Here we show that pri is required for maturation of SCs and for male fecundity, whereas it is not involved in determination of the number of SCs. We provide evidence that Pri acts downstream of Ftz-F1 to regulate maturation but not survival of SCs.
Collapse
Affiliation(s)
- Shinichi Otsune
- Graduate School of Environmental, Life, Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Mirai Matsuka
- Graduate School of Environmental, Life, Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Chisato Shirakashi
- Graduate School of Environmental, Life, Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Xuanshuo Zhang
- Graduate School of Environmental, Life, Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Hideki Nakagoshi
- Graduate School of Environmental, Life, Natural Science and TechnologyOkayama UniversityOkayamaJapan
| |
Collapse
|
3
|
Hsu FY, Yen YP, Fan HC, Chang M, Chen JA. Sertm2 is a conserved micropeptide that promotes GDNF-mediated motor neuron subtype specification. EMBO Rep 2025; 26:2013-2043. [PMID: 40108406 PMCID: PMC12018958 DOI: 10.1038/s44319-025-00400-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 02/04/2025] [Accepted: 02/07/2025] [Indexed: 03/22/2025] Open
Abstract
Small open-reading frame-encoded micropeptides within long noncoding RNAs (lncRNAs) are often overlooked due to their small size and low abundance. However, emerging evidence links these micropeptides to various biological pathways, though their roles in neural development and neurodegeneration remain unclear. Here, we investigate the function of murine micropeptide Sertm2, encoded by the lncRNA A730046J19Rik, during spinal motor neuron (MN) development. Sertm2 is predicted to be a conserved transmembrane protein found in both mouse and human, with subcellular analysis revealing that it is enriched in the cytoplasm and neurites. By generating C terminally Flag-tagged Sertm2 and expressing it from the A730046J19Rik locus, we demonstrate that the Sertm2 micropeptide localizes in spinal MNs in mice. The GDNF signaling-induced Etv4+ motor pool is impaired in Sertm2 knockout mice, which display motor nerve arborization defects that culminate in impaired motor coordination and muscle weakness. Similarly, human SERTM2 knockout iPSC-derived MNs also display reduced ETV4+ motor pools, highlighting that Sertm2 is a novel, evolutionarily conserved micropeptide essential for maintaining GDNF-induced MN subtype identity.
Collapse
Affiliation(s)
- Fang-Yu Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 10617, Taiwan
| | - Ya-Ping Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hung-Chi Fan
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Mien Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 10617, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
4
|
Tong G, Martinez TF. Ribosome profiling reveals hidden world of small proteins. Trends Genet 2025; 41:101-103. [PMID: 39814675 DOI: 10.1016/j.tig.2024.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Accepted: 12/28/2024] [Indexed: 01/18/2025]
Abstract
The development of ribosome profiling (Ribo-seq) by Ingolia et al. introduced a powerful new method for monitoring translation genome-wide. Application of Ribo-seq across multiple organisms has since revealed thousands of unannotated translated small open reading frames (ORFs) and enhanced efforts to study their encoded proteins, called microproteins.
Collapse
Affiliation(s)
- Gregory Tong
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA
| | - Thomas F Martinez
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92617, USA.
| |
Collapse
|
5
|
Tornini VA. Grand roles for microproteins. Nat Rev Mol Cell Biol 2025; 26:84. [PMID: 39543246 DOI: 10.1038/s41580-024-00806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
Affiliation(s)
- Valerie A Tornini
- Department of Integrative Biology and Physiology, Institute for Society and Genetics, University of California, Los Angeles, CA, USA.
| |
Collapse
|
6
|
Baena-Angulo C, Platero AI, Couso JP. Cis to trans: small ORF functions emerging through evolution. Trends Genet 2025; 41:119-131. [PMID: 39603921 DOI: 10.1016/j.tig.2024.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 10/14/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024]
Abstract
Hundreds of thousands of small open reading frames (smORFs) of less than 100 codons exist in every genome, especially in long noncoding RNAs (lncRNAs) and in the 5' leaders of mRNAs. smORFs are often discarded as nonfunctional, but ribosomal profiling (RiboSeq) reveals that thousands are translated, while characterised smORF functions have risen from anecdotal to identifiable trends: smORFs can either have a cis-noncoding regulatory function (involving low translation of nonfunctional peptides) or full coding function mediated by robustly translated peptides, often having cellular and physiological roles as membrane-associated regulators of canonical proteins. The evolutionary context reveals that many smORFs represent new genes emerging de novo from noncoding sequences. We suggest a mechanism for this process, where cis-noncoding smORF functions provide niches for the subsequent evolution of full peptide functions.
Collapse
Affiliation(s)
- Casimiro Baena-Angulo
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain
| | - Ana Isabel Platero
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain
| | - Juan Pablo Couso
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Carretera de Utrera Km1, Sevilla 41013, Spain.
| |
Collapse
|
7
|
Chen S, Liu M, Yi W, Li H, Yu Q. Micropeptides derived from long non-coding RNAs: Computational analysis and functional roles in breast cancer and other diseases. Gene 2025; 935:149019. [PMID: 39461573 DOI: 10.1016/j.gene.2024.149019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 10/08/2024] [Accepted: 10/16/2024] [Indexed: 10/29/2024]
Abstract
Long non-coding RNAs (lncRNAs), once thought to be mere transcriptional noise, are now revealing a hidden code. Recent advancements like ribosome sequencing have unveiled that many lncRNAs harbor small open reading frames and can potentially encode functional micropeptides. Emerging research suggests these micropeptides, not the lncRNAs themselves, play crucial roles in regulating homeostasis, inflammation, metabolism, and especially in breast cancer progression. This review delves into the rapidly evolving computational tools used to predict and validate lncRNA-encoded micropeptides. We then explore the diverse functions and mechanisms of action of these micropeptides in breast cancer pathogenesis, with a focus on their roles in various species. Ultimately, this review aims to illuminate the functional landscape of lncRNA-encoded micropeptides and their potential as therapeutic targets in cancer.
Collapse
Affiliation(s)
- Saisai Chen
- Department of Breast Surgery, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei 230031, China
| | - Mengru Liu
- Department of Infection, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Weizhen Yi
- Department of Breast Surgery, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei 230031, China
| | - Huagang Li
- Department of Breast Surgery, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei 230031, China
| | - Qingsheng Yu
- Institute of Chinese Medicine Surgery, Anhui Academy of Chinese Medicine, Hefei 230031, China.
| |
Collapse
|
8
|
Platero AI, Pueyo JI, Bishop SA, Magny EG, Couso JP. Pervasiveness of Microprotein Function Amongst Drosophila Small Open Reading Frames (SMORFS). Cells 2024; 13:2090. [PMID: 39768181 PMCID: PMC11674832 DOI: 10.3390/cells13242090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/29/2024] [Accepted: 12/09/2024] [Indexed: 01/11/2025] Open
Abstract
Small Open Reading Frames (smORFs) of less than 100 codons remain mostly uncharacterised. About a thousand smORFs per genome encode peptides and microproteins about 70-80 aa long, often containing recognisable protein structures and markers of translation, and these are referred to as short Coding Sequences (sCDSs). The characterisation of individual sCDSs has provided examples of smORFs' function and conservation, but we cannot infer the functionality of all other metazoan smORFs from these. sCDS function has been characterised at a genome-wide scale in yeast and bacteria, showing that hundreds can produce a phenotype, but attempts in metazoans have been less successful. Either most sCDSs are not functional, or classic experimental techniques do not work with smORFs due to their shortness. Here, we combine extensive proteomics with bioinformatics and genetics in order to detect and corroborate sCDS function in Drosophila. Our studies nearly double the number of sCDSs with detected peptides and microproteins and an experimentally corroborated function. Finally, we observe a correlation between proven sCDS protein function and bioinformatic markers such as conservation and GC content. Our results support that sCDSs peptides and microproteins act as membrane-related regulators of canonical proteins, regulators whose functions are best understood at the cellular level, and whose mutants produce little, if any, overt morphological phenotypes.
Collapse
Affiliation(s)
- Ana Isabel Platero
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, CSIC, 41013 Sevilla, Spain; (A.I.P.); (S.A.B.)
| | - Jose Ignacio Pueyo
- Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK;
| | - Sarah Anne Bishop
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, CSIC, 41013 Sevilla, Spain; (A.I.P.); (S.A.B.)
- Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK;
| | - Emile Gerard Magny
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, CSIC, 41013 Sevilla, Spain; (A.I.P.); (S.A.B.)
- Department of Molecular & Cellular Physiology and Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94035, USA
| | - Juan Pablo Couso
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, CSIC, 41013 Sevilla, Spain; (A.I.P.); (S.A.B.)
| |
Collapse
|
9
|
Guan J, Chen X, Li Z, Deng S, Wumaier A, Ma Y, Xie L, Huang S, Zhu Y, Zhuo Y. Role of N6-methyladenosine-related lncRnas in pseudoexfoliation glaucoma. Epigenetics 2024; 19:2348840. [PMID: 38716769 PMCID: PMC11086004 DOI: 10.1080/15592294.2024.2348840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
To explore the role of lncRNA m6A methylation modification in aqueous humour (AH) of patients with pseudoexfoliation glaucoma (PXG). Patients with open-angle PXG under surgery from June 2021 to December 2021 were selected. Age- and gender-matched patients with age-related cataract (ARC) were chosen as control. Patients underwent detailed ophthalmic examinations. 0.05-0.1 ml AH were extracted during surgery for MeRIP-Seq and RNA-Seq. Joint analysis was used to screen lncRNAs with differential m6A methylation modification and expression. Online software tools were used to draw lncRNA-miRNA-mRNA network (ceRNA). Expression of lncRNAs and mRNAs was confirmed using quantitative real-time PCR. A total of 4151 lncRNAs and 4386 associated m6A methylation modified peaks were identified in the PXG group. Similarly, 2490 lncRNAs and 2595 associated m6A methylation modified peaks were detected in the control. Compared to the ARC group, the PXG group had 234 hypermethylated and 402 hypomethylated m6A peaks, with statistically significant differences (| Fold Change (FC) |≥2, p < 0.05). Bioinformatic analysis revealed that these differentially methylated lncRNA enriched in extracellular matrix formation, tight adhesion, TGF- β signalling pathway, AMPK signalling pathway, and MAPK signalling pathway. Joint analysis identified 10 lncRNAs with differential m6A methylation and expression simultaneously. Among them, the expression of ENST000000485383 and ROCK1 were confirmed downregulated in the PXG group by RT-qPCR. m6A methylation modification may affect the expression of lncRNA and participate in the pathogenesis of PXG through the ceRNA network. ENST000000485383-hsa miR592-ROCK1 May be a potential target pathway for further investigation in PXG m6A methylation.
Collapse
Affiliation(s)
- Jieying Guan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaohong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Shuifeng Deng
- The Department of Ophthalmology, Huizhou Hospital Affiliated to Guangzhou Medical University (Huizhou Third People’s Hospital), Huizhou, China
| | - Aizezi Wumaier
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Yuncheng Ma
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Lingling Xie
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Shengsong Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| |
Collapse
|
10
|
Zhao L, Svetec N, Begun DJ. De Novo Genes. Annu Rev Genet 2024; 58:211-232. [PMID: 39088850 PMCID: PMC12051474 DOI: 10.1146/annurev-genet-111523-102413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
Although the majority of annotated new genes in a given genome appear to have arisen from duplication-related mechanisms, recent studies have shown that genes can also originate de novo from ancestrally nongenic sequences. Investigating de novo-originated genes offers rich opportunities to understand the origin and functions of new genes, their regulatory mechanisms, and the associated evolutionary processes. Such studies have uncovered unexpected and intriguing facets of gene origination, offering novel perspectives on the complexity of the genome and gene evolution. In this review, we provide an overview of the research progress in this field, highlight recent advancements, identify key technical and conceptual challenges, and underscore critical questions that remain to be addressed.
Collapse
Affiliation(s)
- Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA; ,
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA; ,
| | - David J Begun
- Department of Evolution and Ecology, University of California, Davis, California, USA;
| |
Collapse
|
11
|
Chanut-Delalande H, Zanet J. Small ORFs, Big Insights: Drosophila as a Model to Unraveling Microprotein Functions. Cells 2024; 13:1645. [PMID: 39404408 PMCID: PMC11475943 DOI: 10.3390/cells13191645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 09/27/2024] [Accepted: 10/02/2024] [Indexed: 10/19/2024] Open
Abstract
Recently developed experimental and computational approaches to identify putative coding small ORFs (smORFs) in genomes have revealed thousands of smORFs localized within coding and non-coding RNAs. They can be translated into smORF peptides or microproteins, which are defined as less than 100 amino acids in length. The identification of such a large number of potential biological regulators represents a major challenge, notably for elucidating the in vivo functions of these microproteins. Since the emergence of this field, Drosophila has proved to be a valuable model for studying the biological functions of microproteins in vivo. In this review, we outline how the smORF field emerged and the nomenclature used in this domain. We summarize the technical challenges associated with identifying putative coding smORFs in the genome and the relevant translated microproteins. Finally, recent findings on one of the best studied smORF peptides, Pri, and other microproteins studied so far in Drosophila are described. These studies highlight the diverse roles that microproteins can fulfil in the regulation of various molecular targets involved in distinct cellular processes during animal development and physiology. Given the recent emergence of the microprotein field and the associated discoveries, the microproteome represents an exquisite source of potentially bioactive molecules, whose in vivo biological functions can be explored in the Drosophila model.
Collapse
Affiliation(s)
| | - Jennifer Zanet
- Unité de Biologie Moléculaire, Cellulaire et du Développement (MCD), UMR 5077, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, 31062 Toulouse, France;
| |
Collapse
|
12
|
Garcia-Del Rio DF, Derhourhi M, Bonnefond A, Leblanc S, Guilloy N, Roucou X, Eyckerman S, Gevaert K, Salzet M, Cardon T. Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization. Cell Death Dis 2024; 15:712. [PMID: 39349928 PMCID: PMC11442847 DOI: 10.1038/s41419-024-07046-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024]
Abstract
Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has a high potential to unravel the characteristics, variants, expression levels of the alternative proteome, in addition to already annotated proteins (RefProts). To obtain a broader view of the proteome of ovarian cancer cells compared to ovarian epithelial cells, cell-specific total RNA-sequencing profiles and customized protein databases were generated. In total, 128 RefProts and 30 AltProts were identified exclusively in SKOV-3 and PEO-4 cells. Among them, an AltProt variant of IP_715944, translated from DHX8, was found mutated (p.Leu44Pro). We show high variation in protein expression levels of RefProts and AltProts in different subcellular compartments. The presence of 117 RefProt and two AltProt variants was described, along with their possible implications in the different physiological/pathological characteristics. To identify the possible involvement of AltProts in cellular processes, cross-linking-MS (XL-MS) was performed in each cell line to identify AltProt-RefProt interactions. This approach revealed an interaction between POLD3 and the AltProt IP_183088, which after molecular docking, was placed between POLD3-POLD2 binding sites, highlighting its possibility of the involvement in DNA replication and repair.
Collapse
Affiliation(s)
- Diego Fernando Garcia-Del Rio
- Univ. Lille, Inserm, CHU Lille, U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Mehdi Derhourhi
- Université de Lille, Inserm/CNRS UMR 1283/8199, Pasteur Institute of Lille, EGID, Lille, France University of Lille, Lille, France
| | - Amelie Bonnefond
- Université de Lille, Inserm/CNRS UMR 1283/8199, Pasteur Institute of Lille, EGID, Lille, France University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Sébastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, J1E4K8, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, J1E4K8, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, J1E4K8, Canada
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
| | - Tristan Cardon
- Univ. Lille, Inserm, CHU Lille, U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
| |
Collapse
|
13
|
Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. BIOPHYSICAL REPORTS 2024; 4:100167. [PMID: 38909903 PMCID: PMC11305224 DOI: 10.1016/j.bpr.2024.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/09/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. In addition, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from noncoding ones in otherwise ambiguous cases.
Collapse
Affiliation(s)
- A M Whited
- BioFrontiers Institute, University of Colorado, Boulder, Colorado
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts
| | - Jeffre Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | | | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts
| | - John L Rinn
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Physics, University of Colorado Boulder, Boulder, Colorado.
| |
Collapse
|
14
|
Camilleri-Robles C, Amador R, Tiebe M, Teleman A, Serras F, Guigó R, Corominas M. Long non-coding RNAs involved in Drosophila development and regeneration. NAR Genom Bioinform 2024; 6:lqae091. [PMID: 39157585 PMCID: PMC11327875 DOI: 10.1093/nargab/lqae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024] Open
Abstract
The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been identified as regulators of multiple biological processes, including chromatin structure, gene expression, splicing, mRNA degradation, and translation. However, functional studies of lncRNAs are hindered by the usual lack of phenotypes upon deletion or inhibition. Here, we used Drosophila imaginal discs as a model system to identify lncRNAs involved in development and regeneration. We examined a subset of lncRNAs expressed in the wing, leg, and eye disc development. Additionally, we analyzed transcriptomic data from regenerating wing discs to profile the expression pattern of lncRNAs during tissue repair. We focused on the lncRNA CR40469, which is upregulated during regeneration. We generated CR40469 mutant flies that developed normally but showed impaired wing regeneration upon cell death induction. The ability of these mutants to regenerate was restored by the ectopic expression of CR40469. Furthermore, we found that the lncRNA CR34335 has a high degree of sequence similarity with CR40469 and can partially compensate for its function during regeneration in the absence of CR40469. Our findings point to a potential role of the lncRNA CR40469 in trans during the response to damage in the wing imaginal disc.
Collapse
Affiliation(s)
- Carlos Camilleri-Robles
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Raziel Amador
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marcel Tiebe
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Florenci Serras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Montserrat Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| |
Collapse
|
15
|
Silva CAO, Alves SDS, Rodrigues BDC, Fraga Egidio JA, Ribeiro L, Logullo C, Mury FB, Santos DDG, Portal T, Monteiro-de-Barros C, Roberto da Silva J, Nepomuceno-Silva JL, Nunes-da-Fonseca R. The mlpt smORF gene is essential for digestive physiology and molting during nymphal stages in the kissing bug Rhodnius prolixus. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 172:104154. [PMID: 38972513 DOI: 10.1016/j.ibmb.2024.104154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Chagas disease affects around 8 million people globally, with Latin America bearing approximately 10,000 deaths each year. Combatting the disease relies heavily on vector control methods, necessitating the identification of new targets. Within insect genomes, genes harboring small open reading frames (smORFs - < 100 amino acids) present numerous potential candidates. In our investigation, we elucidate the pivotal role of the archetypal smORF-containing gene, mille-pattes/polished-rice/tarsalless (mlpt/pri/tal), in the post-embryonic development of the kissing bug Rhodnius prolixus. Injection of double-stranded RNA targeting mlpt (dsmlpt) during nymphal stages yields a spectrum of phenotypes hindering post-embryonic growth. Notably, fourth or fifth stage nymphs subjected to dsmlpt do not undergo molting. These dsmlpt nymphs display heightened mRNA levels of JHAMT-like and EPOX-like, enzymes putatively involved in the juvenile hormone (JH) pathway, alongside increased expression of the transcription factor Kr-h1, indicating changes in the hormonal control. Histological examination reveals structural alterations in the hindgut and external cuticle of dsmlpt nymphs compared to control (dsGFP) counterparts. Furthermore, significant changes in the vector's digestive physiology were observed, with elevated hemozoin and glucose levels in the posterior midgut of dsmlpt nymphs. Importantly, dsmlpt nymphs exhibit impaired metacyclogenesis of Trypanosoma cruzi, the causative agent of Chagas disease, underscoring the crucial role of proper gut organization in parasite differentiation. Thus, our findings constitute the first evidence of a smORF-containing gene's regulatory influence on vector physiology, parasitic cycle, and disease transmission.
Collapse
Affiliation(s)
- Carina Azevedo Oliveira Silva
- Laboratório Integrado de Bioquímica Hatisaburo Masuda (LIBHM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil; Laboratório Integrado de Ciências Morfofuncionais (LICM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Sandy da Silveira Alves
- Laboratório Integrado de Biociências Translacionais (LIBT), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Bruno da Costa Rodrigues
- Laboratório Integrado de Ciências Morfofuncionais (LICM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Jonatha Anderson Fraga Egidio
- Laboratório Integrado de Ciências Morfofuncionais (LICM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Lupis Ribeiro
- Laboratório Integrado de Ciências Morfofuncionais (LICM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Carlos Logullo
- Laboratório Integrado de Bioquímica Hatisaburo Masuda (LIBHM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Brazil
| | - Flavia Borges Mury
- Laboratório Integrado de Biociências Translacionais (LIBT), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Brazil
| | - Daniele das Graças Santos
- Laboratório Integrado de Ciências Morfofuncionais (LICM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Taynan Portal
- Laboratório Integrado de Biociências Translacionais (LIBT), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Cintia Monteiro-de-Barros
- Laboratório Integrado de Biociências Translacionais (LIBT), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - José Roberto da Silva
- Laboratório Integrado de Bioquímica Hatisaburo Masuda (LIBHM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Brazil
| | - José Luciano Nepomuceno-Silva
- Laboratório Integrado de Bioquímica Hatisaburo Masuda (LIBHM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Rodrigo Nunes-da-Fonseca
- Laboratório Integrado de Ciências Morfofuncionais (LICM), Instituto de Biodiversidade e Sustentabilidade (NUPEM/UFRJ), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular - INCT-EM, Brazil.
| |
Collapse
|
16
|
Ding S, Liao H, Huang F, Chen L, Guo W, Feng K, Huang T, Cai YD. Analyzing domain features of small proteins using a machine-learning method. Proteomics 2024; 24:e2300302. [PMID: 38258387 DOI: 10.1002/pmic.202300302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Small proteins (SPs) are a unique group of proteins that play crucial roles in many important biological processes. Exploring the biological function of SPs is necessary. In this study, the InterPro tool and the maximum correlation method were utilized to analyze functional domains of SPs. The purpose was to identify important functional domains that can indicate the essential differences between small and large protein sequences. First, the small and large proteins were represented by their functional domains via a one-hot scheme. Then, the MaxRel method was adopted to evaluate the relationships between each domain and the target variable, indicating small or large protein. The top 36 domain features were selected for further investigation. Among them, 14 were deemed to be highly related to SPs because they were annotated to SPs more frequently than large proteins. We found the involvement of functional domains, such as ubiquitin-conjugating enzyme/RWD-like, nuclear transport factor 2 domain, and alpha subunit of guanine nucleotide-binding protein (G-protein) in regulating the biological function of SPs. The involvement of these domains has been confirmed by other recent studies. Our findings indicate that protein functional domains may regulate small protein-related functions and predict their biological activity.
Collapse
Affiliation(s)
- ShiJian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | | | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
| |
Collapse
|
17
|
Jaiswal M, Kumar S. smAMPsTK: a toolkit to unravel the smORFome encoding AMPs of plant species. J Biomol Struct Dyn 2024; 42:6600-6612. [PMID: 37464885 DOI: 10.1080/07391102.2023.2235605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
The pervasive repertoire of plant molecules with the potential to serve as a substitute for conventional antibiotics has led to obtaining better insights into plant-derived antimicrobial peptides (AMPs). The massive distribution of Small Open Reading Frames (smORFs) throughout eukaryotic genomes with proven extensive biological functions reflects their practicality as antimicrobials. Here, we have developed a pipeline named smAMPsTK to unveil the underlying hidden smORFs encoding AMPs for plant species. By applying this pipeline, we have elicited AMPs of various functional activity of lengths ranging from 5 to 100 aa by employing publicly available transcriptome data of five different angiosperms. Later, we studied the coding potential of AMPs-smORFs, the inclusion of diverse translation initiation start codons, and amino acid frequency. Codon usage study signifies no such codon usage biases for smORFs encoding AMPs. Majorly three start codons are prominent in generating AMPs. The evolutionary and conservational study proclaimed the widespread distribution of AMPs encoding genes throughout the plant kingdom. Domain analysis revealed that nearly all AMPs have chitin-binding ability, establishing their role as antifungal agents. The current study includes a developed methodology to characterize smORFs encoding AMPs, and their implications as antimicrobial, antibacterial, antifungal, or antiviral provided by SVM score and prediction status calculated by machine learning-based prediction models. The pipeline, complete package, and the results derived for five angiosperms are freely available at https://github.com/skbinfo/smAMPsTK.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mohini Jaiswal
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
18
|
Perdikopanis N, Giannakakis A, Kavakiotis I, Hatzigeorgiou AG. D-sORF: Accurate Ab Initio Classification of Experimentally Detected Small Open Reading Frames (sORFs) Associated with Translational Machinery. BIOLOGY 2024; 13:563. [PMID: 39194501 DOI: 10.3390/biology13080563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024]
Abstract
Small open reading frames (sORFs; <300 nucleotides or <100 amino acids) are widespread across all genomes, and an increasing variety of them appear to be translating from non-genic regions. Over the past few decades, peptides produced from sORFs have been identified as functional in various organisms, from bacteria to humans. Despite recent advances in next-generation sequencing and proteomics, accurate annotation and classification of sORFs remain a rate-limiting step toward reliable and high-throughput detection of small proteins from non-genic regions. Additionally, the cost of computational methods utilizing machine learning is lower than that of biological experiments, and they can be employed to detect sORFs, laying the groundwork for biological experiments. We present D-sORF, a machine-learning framework that integrates the statistical nucleotide context and motif information around the start codon to predict coding sORFs. D-sORF scores directly for coding identity and requires only the underlying genomic sequence, without incorporating parameters such as the conservation, which, in the case of sORFs, may increase the dispersion of scores within the significantly less conserved non-genic regions. D-sORF achieves 94.74% precision and 92.37% accuracy for small ORFs (using the 99 nt medium length window). When D-sORF is applied to sORFs associated with ribosomes, the identification of transcripts producing peptides (annotated by the Ensembl IDs) is similar to or superior to experimental methodologies based on ribosome-sequencing (Ribo-Seq) profiling. In parallel, the recognition of putative negative data, such as the intron-containing transcripts that associate with ribosomes, remains remarkably low, indicating that D-sORF could be efficiently applied to filter out false-positive sORFs from Ribo-Seq data because of the non-productive ribosomal binding or noise inherent in these protocols.
Collapse
Affiliation(s)
- Nikos Perdikopanis
- Department of Electrical and Computer Engineering, University of Thessaly, 38221 Volos, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 38221 Volos, Greece
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Ioannis Kavakiotis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 38221 Volos, Greece
| | - Artemis G Hatzigeorgiou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 38221 Volos, Greece
- Hellenic Pasteur Institute, 11521 Athens, Greece
| |
Collapse
|
19
|
Shanthappa PM, Suravajhala R, Kumar G, Melethadathil N. Computational exploration of novel antimicrobial modalities targeting fucose-binding lectins and ribosomes in Mycobacterium smegmatis using tRNA-encoded peptides. J Biomol Struct Dyn 2024:1-13. [PMID: 38676533 DOI: 10.1080/07391102.2024.2335555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/19/2024] [Indexed: 04/29/2024]
Abstract
tRNA-Encoded Peptides (tREPs), encoded by small open reading frames (smORFs) within tRNA genes, have recently emerged as a new class of functional peptides exhibiting antiparasitic activity. The discovery of tREPs has led to a re-evaluation of the role of tRNAs in biology and has expanded our understanding of the genetic code. This presents an immense, unexplored potential in the realm of tRNA-peptide interactions, paving the way for groundbreaking discoveries and innovative applications in various biological functions. This study explores the antimicrobial potential of tREPs against protein targets by employing a computational method that uses verified data sources and highly recognized predictive algorithms to provide a sorted list of likely antimicrobial peptides, which were then filtered for toxicity, cell permeability, allergenicity and half-life. These peptides were then docked with screened protein targets and computationally validated using molecular dynamics (MD) simulations for 150 ns and the binding free energy was estimated. The peptides Pep2 (VVLWRKPRVRKTG) and Pep6 (HRLRLRRRKPWW) exhibited good binding affinities of -110.5 +/- 2.5 and -129.0 +/- 3.9, respectively, with RMSD values of 0.4 and 0.25 nm against the fucose-binding lectin (7NEF) and the 30S ribosome of Mycobacterium smegmatis (5O5J) protein targets. The 7NEF-Pep2 and 5O5J-Pep6 complexes indicated higher negative binding free energies of -52.55 kcal/mol and -55.52 kcal/mol respectively, as calculated by Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA). Thus, the tREPs derived peptides designed as a part of this study, provide novel approaches for potential anti-bacterial therapeutic modalities.
Collapse
Affiliation(s)
- Pallavi M Shanthappa
- Department of Computer Science, School of Computing, Amrita Vishwa Vidyapeetham, Mysuru, India
| | | | - Geetha Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, India
| | | |
Collapse
|
20
|
Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589296. [PMID: 38659920 PMCID: PMC11042228 DOI: 10.1101/2024.04.12.589296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. Additionally, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from non-coding ones in otherwise ambiguous cases.
Collapse
Affiliation(s)
- A M Whited
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Jeffre Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Biochemistry, University of Colorado Boulder, CO, USA
| | | | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - John L Rinn
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Biochemistry, University of Colorado Boulder, CO, USA
| | - Loren E Hough
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado Boulder, CO, USA
| |
Collapse
|
21
|
Appleby S, Aitken-Buck HM, Holdaway MS, Byers MS, Frampton CM, Paton LN, Richards AM, Lamberts RR, Pemberton CJ. Cardiac effects of myoregulin in ischemia-reperfusion. Peptides 2024; 174:171156. [PMID: 38246425 DOI: 10.1016/j.peptides.2024.171156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Myoregulin is a recently discovered micropeptide that controls calcium levels by inhibiting the intracellular calcium pump sarco-endoplasmic reticulum Ca2+-ATPase (SERCA). Keeping calcium levels balanced in the heart is essential for normal heart functioning, thus myoregulin has the potential to be a crucial regulator of cardiac muscle performance by reducing the rate of intracellular Ca2+ uptake. We provide the first report of myoregulin mRNA expression in human heart tissue, absence of expression in human plasma, and the effects of myoregulin on cardiac hemodynamics in an ex vivo Langendorff isolated rat heart model of ischemia/reperfusion. In this preliminary study, myoregulin provided a cardio-protective effect, as assessed by preservation of left ventricular contractility and relaxation, during ischemia/reperfusion. This study provides the foundation for future research in this area.
Collapse
Affiliation(s)
- Sarah Appleby
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - Hamish M Aitken-Buck
- Department of Physiology, HeartOtago, University of Otago, 270 Great King St, Dunedin 9016, New Zealand.
| | - Mark S Holdaway
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - Mathew S Byers
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - Chris M Frampton
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - Louise N Paton
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| | - A Mark Richards
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand; Department of Cardiology, Te Whatu Ora Waitaha, 2 Riccarton Avenue, Christchurch 8011, New Zealand; Cardiovascular Research Institute, National University of Singapore, 1E Kent Ridge Road, Singapore.
| | - Regis R Lamberts
- Department of Physiology, HeartOtago, University of Otago, 270 Great King St, Dunedin 9016, New Zealand.
| | - Christopher J Pemberton
- Christchurch Heart Institute, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand.
| |
Collapse
|
22
|
Romero-Becera R, Santamans AM, Arcones AC, Sabio G. From Beats to Metabolism: the Heart at the Core of Interorgan Metabolic Cross Talk. Physiology (Bethesda) 2024; 39:98-125. [PMID: 38051123 DOI: 10.1152/physiol.00018.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/26/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023] Open
Abstract
The heart, once considered a mere blood pump, is now recognized as a multifunctional metabolic and endocrine organ. Its function is tightly regulated by various metabolic processes, at the same time it serves as an endocrine organ, secreting bioactive molecules that impact systemic metabolism. In recent years, research has shed light on the intricate interplay between the heart and other metabolic organs, such as adipose tissue, liver, and skeletal muscle. The metabolic flexibility of the heart and its ability to switch between different energy substrates play a crucial role in maintaining cardiac function and overall metabolic homeostasis. Gaining a comprehensive understanding of how metabolic disorders disrupt cardiac metabolism is crucial, as it plays a pivotal role in the development and progression of cardiac diseases. The emerging understanding of the heart as a metabolic and endocrine organ highlights its essential contribution to whole body metabolic regulation and offers new insights into the pathogenesis of metabolic diseases, such as obesity, diabetes, and cardiovascular disorders. In this review, we provide an in-depth exploration of the heart's metabolic and endocrine functions, emphasizing its role in systemic metabolism and the interplay between the heart and other metabolic organs. Furthermore, emerging evidence suggests a correlation between heart disease and other conditions such as aging and cancer, indicating that the metabolic dysfunction observed in these conditions may share common underlying mechanisms. By unraveling the complex mechanisms underlying cardiac metabolism, we aim to contribute to the development of novel therapeutic strategies for metabolic diseases and improve overall cardiovascular health.
Collapse
Affiliation(s)
| | | | - Alba C Arcones
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Guadalupe Sabio
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| |
Collapse
|
23
|
Gallois M, Menoret D, Marques-Prieto S, Montigny A, Valenti P, Moussian B, Plaza S, Payre F, Chanut-Delalande H. Pri peptides temporally coordinate transcriptional programs during epidermal differentiation. SCIENCE ADVANCES 2024; 10:eadg8816. [PMID: 38335295 PMCID: PMC10857433 DOI: 10.1126/sciadv.adg8816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
To achieve a highly differentiated state, cells undergo multiple transcriptional processes whose coordination and timing are not well understood. In Drosophila embryonic epidermal cells, polished-rice (Pri) smORF peptides act as temporal mediators of ecdysone to activate a transcriptional program leading to cell shape remodeling. Here, we show that the ecdysone/Pri axis concomitantly represses the transcription of a large subset of cuticle genes to ensure proper differentiation of the insect exoskeleton. The repression relies on the transcription factor Ken and persists for several days throughout early larval stages, during which a soft cuticle allows larval crawling. The onset of these cuticle genes normally awaits the end of larval stages when the rigid pupal case assembles, and their premature expression triggers abnormal sclerotization of the larval cuticle. These results uncovered a temporal switch to set up distinct structures of cuticles adapted to the animal lifestyle and which might be involved in the evolutionary history of insects.
Collapse
Affiliation(s)
- Maylis Gallois
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Delphine Menoret
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Simon Marques-Prieto
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Audrey Montigny
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Philippe Valenti
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Bernard Moussian
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, CNRS/UPS/INPT, Auzeville-Tolosane, France
| | - François Payre
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Hélène Chanut-Delalande
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| |
Collapse
|
24
|
Sahgal A, Uversky V, Davé V. Microproteins transitioning into a new Phase: Defining the undefined. Methods 2023; 220:38-54. [PMID: 37890707 DOI: 10.1016/j.ymeth.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Recent advancements in omics technologies have unveiled a hitherto unknown group of short polypeptides called microproteins (miPs). Despite their size, accumulating evidence has demonstrated that miPs exert varied and potent biological functions. They act in paracrine, juxtracrine, and endocrine fashion, maintaining cellular physiology and driving diseases. The present study focuses on biochemical and biophysical analysis and characterization of twenty-four human miPs using distinct computational methods, including RIDAO, AlphaFold2, D2P2, FuzDrop, STRING, and Emboss Pep wheel. miPs often lack well-defined tertiary structures and may harbor intrinsically disordered regions (IDRs) that play pivotal roles in cellular functions. Our analyses define the physicochemical properties of an essential subset of miPs, elucidating their structural characteristics and demonstrating their propensity for driving or participating in liquid-liquid phase separation (LLPS) and intracellular condensate formation. Notably, miPs such as NoBody and pTUNAR revealed a high propensity for LLPS, implicating their potential involvement in forming membrane-less organelles (MLOs) during intracellular LLPS and condensate formation. The results of our study indicate that miPs have functionally profound implications in cellular compartmentalization and signaling processes essential for regulating normal cellular functions. Taken together, our methodological approach explains and highlights the biological importance of these miPs, providing a deeper understanding of the unusual structural landscape and functionality of these newly defined small proteins. Understanding their functions and biological behavior will aid in developing targeted therapies for diseases that involve miPs.
Collapse
Affiliation(s)
- Aayushi Sahgal
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vrushank Davé
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Pathology and Cell Biology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States.
| |
Collapse
|
25
|
Mohsen JJ, Martel AA, Slavoff SA. Microproteins-Discovery, structure, and function. Proteomics 2023; 23:e2100211. [PMID: 37603371 PMCID: PMC10841188 DOI: 10.1002/pmic.202100211] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Advances in proteogenomic technologies have revealed hundreds to thousands of translated small open reading frames (sORFs) that encode microproteins in genomes across evolutionary space. While many microproteins have now been shown to play critical roles in biology and human disease, a majority of recently identified microproteins have little or no experimental evidence regarding their functionality. Computational tools have some limitations for analysis of short, poorly conserved microprotein sequences, so additional approaches are needed to determine the role of each member of this recently discovered polypeptide class. A currently underexplored avenue in the study of microproteins is structure prediction and determination, which delivers a depth of functional information. In this review, we provide a brief overview of microprotein discovery methods, then examine examples of microprotein structures (and, conversely, intrinsic disorder) that have been experimentally determined using crystallography, cryo-electron microscopy, and NMR, which provide insight into their molecular functions and mechanisms. Additionally, we discuss examples of predicted microprotein structures that have provided insight or context regarding their function. Analysis of microprotein structure at the angstrom level, and confirmation of predicted structures, therefore, has potential to identify translated microproteins that are of biological importance and to provide molecular mechanism for their in vivo roles.
Collapse
Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alina A. Martel
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| |
Collapse
|
26
|
Bosch JA, Keith N, Escobedo F, Fisher WW, LaGraff JT, Rabasco J, Wan KH, Weiszmann R, Hu Y, Kondo S, Brown JB, Perrimon N, Celniker SE. Molecular and functional characterization of the Drosophila melanogaster conserved smORFome. Cell Rep 2023; 42:113311. [PMID: 37889754 PMCID: PMC10843857 DOI: 10.1016/j.celrep.2023.113311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/24/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Short polypeptides encoded by small open reading frames (smORFs) are ubiquitously found in eukaryotic genomes and are important regulators of physiology, development, and mitochondrial processes. Here, we focus on a subset of 298 smORFs that are evolutionarily conserved between Drosophila melanogaster and humans. Many of these smORFs are conserved broadly in the bilaterian lineage, and ∼182 are conserved in plants. We observe remarkably heterogeneous spatial and temporal expression patterns of smORF transcripts-indicating wide-spread tissue-specific and stage-specific mitochondrial architectures. In addition, an analysis of annotated functional domains reveals a predicted enrichment of smORF polypeptides localizing to mitochondria. We conduct an embryonic ribosome profiling experiment and find support for translation of 137 of these smORFs during embryogenesis. We further embark on functional characterization using CRISPR knockout/activation, RNAi knockdown, and cDNA overexpression, revealing diverse phenotypes. This study underscores the importance of identifying smORF function in disease and phenotypic diversity.
Collapse
Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan Keith
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Felipe Escobedo
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - William W Fisher
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James Thai LaGraff
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jorden Rabasco
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth H Wan
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard Weiszmann
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shu Kondo
- Laboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - James B Brown
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Susan E Celniker
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| |
Collapse
|
27
|
Zhang M, Zhao Y, Liu X, Ruan X, Wang P, Liu L, Wang D, Dong W, Yang C, Xue Y. Pseudogene MAPK6P4-encoded functional peptide promotes glioblastoma vasculogenic mimicry development. Commun Biol 2023; 6:1059. [PMID: 37853052 PMCID: PMC10584926 DOI: 10.1038/s42003-023-05438-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Glioma is the most common primary malignancy of the central nervous system. Glioblastoma (GBM) has the highest degree of malignancy among the gliomas and the strongest resistance to chemotherapy and radiotherapy. Vasculogenic mimicry (VM) provides tumor cells with a blood supply independent of endothelial cells and greatly restricts the therapeutic effect of anti-angiogenic tumor therapy for glioma patients. Vascular endothelial growth factor receptor 2 (VEGFR2) and vascular endothelial cadherin (VE-cadherin) are currently recognized molecular markers of VM in tumors. In the present study, we show that pseudogene MAPK6P4 deficiency represses VEGFR2 and VE-cadherin protein expression levels, as well as inhibits the proliferation, migration, invasion, and VM development of GBM cells. The MAPK6P4-encoded functional peptide P4-135aa phosphorylates KLF15 at the S238 site, promoting KLF15 protein stability and nuclear entry to promote GBM VM formation. KLF15 was further confirmed as a transcriptional activator of LDHA, where LDHA binds and promotes VEGFR2 and VE-cadherin lactylation, thereby increasing their protein expression. Finally, we used orthotopic and subcutaneous xenografted nude mouse models of GBM to verify the inhibitory effect of the above factors on GBM VM development. In summary, this study may represent new targets for the comprehensive treatment of glioma.
Collapse
Affiliation(s)
- Mengyang Zhang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, PR China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, PR China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, PR China
| | - Yubo Zhao
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, PR China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, PR China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, PR China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, PR China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, PR China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, PR China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, PR China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, PR China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, PR China
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, PR China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, PR China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, PR China
| | - Libo Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, PR China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, PR China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, PR China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, PR China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, PR China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, PR China
| | - Weiwei Dong
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, PR China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, PR China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, PR China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, PR China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, PR China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, PR China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, PR China.
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, PR China.
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, PR China.
| |
Collapse
|
28
|
Markus D, Pelletier A, Boube M, Port F, Boutros M, Payre F, Obermayer B, Zanet J. The pleiotropic functions of Pri smORF peptides synchronize leg development regulators. PLoS Genet 2023; 19:e1011004. [PMID: 37903161 PMCID: PMC10635573 DOI: 10.1371/journal.pgen.1011004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/09/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023] Open
Abstract
The last decade witnesses the emergence of the abundant family of smORF peptides, encoded by small ORF (<100 codons), whose biological functions remain largely unexplored. Bioinformatic analyses here identify hundreds of putative smORF peptides expressed in Drosophila imaginal leg discs. Thanks to a functional screen in leg, we found smORF peptides involved in morphogenesis, including the pioneer smORF peptides Pri. Since we identified its target Ubr3 in the epidermis and pri was known to control leg development through poorly understood mechanisms, we investigated the role of Ubr3 in mediating pri function in leg. We found that pri plays several roles during leg development both in patterning and in cell survival. During larval stage, pri activates independently of Ubr3 tarsal transcriptional programs and Notch and EGFR signaling pathways, whereas at larval pupal transition, Pri peptides cooperate with Ubr3 to insure cell survival and leg morphogenesis. Our results highlight Ubr3 dependent and independent functions of Pri peptides and their pleiotropy. Moreover, we reveal that the smORF peptide family is a reservoir of overlooked developmental regulators, displaying distinct molecular functions and orchestrating leg development.
Collapse
Affiliation(s)
- Damien Markus
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Aurore Pelletier
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Muriel Boube
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Fillip Port
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - François Payre
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Benedikt Obermayer
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité Universitätsmedizin-Berlin, Berlin, Germany
| | - Jennifer Zanet
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| |
Collapse
|
29
|
Kulkarni P, Salgia R, Rangarajan G. Intrinsically disordered proteins and conformational noise: The hypothesis a decade later. iScience 2023; 26:107109. [PMID: 37408690 PMCID: PMC10319216 DOI: 10.1016/j.isci.2023.107109] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
Phenotypic plasticity is the ability of individual genotypes to produce different phenotypes in response to environmental perturbations. We previously postulated how conformational noise emanating from conformational dynamics of intrinsically disordered proteins (IDPs) which is distinct from transcriptional noise, can contribute to phenotypic switching by rewiring the cellular protein interaction network. Since most transcription factors are IDPs, we posited that conformational noise is an integral component of transcriptional noise implying that IDPs may amplify total noise in the system either stochastically or in response to environmental changes. Here, we review progress in elucidating the details of the hypothesis. We highlight empirical evidence supporting the hypothesis, discuss conceptual advances that underscore its fundamental importance and implications, and identify areas for future investigations.
Collapse
Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
30
|
Dong X, Zhang K, Xun C, Chu T, Liang S, Zeng Y, Liu Z. Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World. Int J Mol Sci 2023; 24:10562. [PMID: 37445739 DOI: 10.3390/ijms241310562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Small open reading frames (sORFs) are often overlooked features in genomes. In the past, they were labeled as noncoding or "transcriptional noise". However, accumulating evidence from recent years suggests that sORFs may be transcribed and translated to produce sORF-encoded polypeptides (SEPs) with less than 100 amino acids. The vigorous development of computational algorithms, ribosome profiling, and peptidome has facilitated the prediction and identification of many new SEPs. These SEPs were revealed to be involved in a wide range of basic biological processes, such as gene expression regulation, embryonic development, cellular metabolism, inflammation, and even carcinogenesis. To effectively understand the potential biological functions of SEPs, we discuss the history and development of the newly emerging research on sORFs and SEPs. In particular, we review a range of recently discovered bioinformatics tools for identifying, predicting, and validating SEPs as well as a variety of biochemical experiments for characterizing SEP functions. Lastly, this review underlines the challenges and future directions in identifying and validating sORFs and their encoded micropeptides, providing a significant reference for upcoming research on sORF-encoded peptides.
Collapse
Affiliation(s)
- Xiaoping Dong
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Kun Zhang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Chengfeng Xun
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Tianqi Chu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Songping Liang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Yong Zeng
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zhonghua Liu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| |
Collapse
|
31
|
Ni Ong S, Chin Tan B, Hanada K, How Teo C. Unearth of small open reading frames (sORFs) in drought stress transcriptome of Oryza sativa subsp. indica. Gene 2023:147579. [PMID: 37336274 DOI: 10.1016/j.gene.2023.147579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Drought is a major abiotic stress that influences rice production. Although the transcriptomic data of rice against drought is widely available, the regulation of small open reading frames (sORFs) in response to drought stress in rice is yet to be investigated. Different levels of drought stress have different regulatory mechanisms in plants. In this study, drought stress was imposed on four-leaf stage rice, divided into two treatments, 40% and 30% soil moisture content (SMC). The RNAs of the samples were extracted, followed by the RNA sequencing analysis on their sORF expression changes under 40%_SMC and 30%_SMC, and lastly, the expression was validated through NanoString. A total of 122 and 143 sORFs were differentially expressed (DE) in 40%_SMC and 30%_SMC, respectively. In 40%_SMC, 69 sORFs out of 696 (9%) DEGs were found to be upregulated. On the other hand, 69 sORFs out of 449 DEGs (11%) were significantly downregulated. The trend seemed to be higher in 30%_SMC, where 112 (12%) sORFs were found to be upregulated from 928 significantly upregulated DEGs. However, only 8% (31 sORFs out of 385 DEGs) sORFs were downregulated in 30%_SMC. Among the identified sORFs, 110 sORFs with high similarity to rice proteome in the PsORF database were detected in 40%_SMC, while 126 were detected in 30%_SMC. The Gene Ontology (GO) enrichment analysis of DE sORFs revealed their involvement in defense-related biological processes, such as defense response, response to biotic stimulus, and cellular homeostasis, whereas enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that DE sORFs were associated with tryptophan and phenylalanine metabolisms. Several DE sORFs were identified, including the top five sORFs (OsisORF_3394, OsisORF_0050, OsisORF_3007, OsisORF_6407, and OsisORF_7805), which have yet to be characterised. Since these sORFs were responsive to drought stress, they might hold significant potential as targets for future climate-resilient rice development.
Collapse
Affiliation(s)
- Sheue Ni Ong
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka‑shi, Fukuoka 820‑8502, Japan
| | - Chee How Teo
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
| |
Collapse
|
32
|
Lyu Y, Tan B, Li L, Liang R, Lei K, Wang K, Wu D, Lin H, Wang M. A novel protein encoded by circUBE4B promotes progression of esophageal squamous cell carcinoma by augmenting MAPK/ERK signaling. Cell Death Dis 2023; 14:346. [PMID: 37264022 DOI: 10.1038/s41419-023-05865-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 04/23/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023]
Abstract
Esophageal squamous carcinoma (ESCC) is a common malignant cancer. Although the non-coding roles of circRNAs in the pathogenesis of human tumors have been well studied, whether circRNAs participate in the progression of ESCC by encoding novel proteins remains unclear. In this study, we identified an overexpression circRNA with protein-coding ability in ESCC tissues, called circUBE4B, whose expression level is correlated with tumor size and tumor differentiation level of ESCC patients. Moreover, a higher level of circUBE4B in ESCC patients is correlated with a worse prognosis. Functionally, we found that circUBE4B promoted the proliferation of ESCC cells by encoding a novel cancer-promoting protein, circUBE4B-173aa. Mechanistically, the circUBE4B-173aa protein interacts with MAPK1 and promotes the phosphorylation level of MAPK1 to eventually activate MAPK/ERK signaling pathway. The xenograft model revealed that overexpression of circUBE4B-173aa in ESCC cells significantly promoted the growth of grafts. Our study provides new insights into the mechanism of circRNA in the development of ESCC and circUBE4B-173aa has the potential to serve as a biomarker and a novel therapeutic target for ESCC therapy.
Collapse
Affiliation(s)
- Yingcheng Lyu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Binghua Tan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Lin Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Ruihao Liang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Kai Lei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Kefeng Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Duoguang Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Huayue Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
| | - Minghui Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
| |
Collapse
|
33
|
Wang Z, Cui Q, Su C, Zhao S, Wang R, Wang Z, Meng J, Luan Y. Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress. Int J Biol Macromol 2023:124952. [PMID: 37257526 DOI: 10.1016/j.ijbiomac.2023.124952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.
Collapse
Affiliation(s)
- Zhengjie Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qi Cui
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ruiming Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
| |
Collapse
|
34
|
Inchingolo MA, Diman A, Adamczewski M, Humphreys T, Jaquier-Gubler P, Curran JA. TP53BP1, a dual-coding gene, uses promoter switching and translational reinitiation to express a smORF protein. iScience 2023; 26:106757. [PMID: 37216125 PMCID: PMC10193022 DOI: 10.1016/j.isci.2023.106757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/07/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
The complexity of the metazoan proteome is significantly increased by the expression of small proteins (<100 aa) derived from smORFs within lncRNAs, uORFs, 3' UTRs and, reading frames overlapping the CDS. These smORF encoded proteins (SEPs) have diverse roles, ranging from the regulation of cellular physiological to essential developmental functions. We report the characterization of a new member of this protein family, SEP53BP1, derived from a small internal ORF that overlaps the CDS encoding 53BP1. Its expression is coupled to the utilization of an alternative, cell-type specific promoter coupled to translational reinitiation events mediated by a uORF in the alternative 5' TL of the mRNA. This uORF-mediated reinitiation at an internal ORF is also observed in zebrafish. Interactome studies indicate that the human SEP53BP1 associates with components of the protein turnover pathway including the proteasome, and the TRiC/CCT chaperonin complex, suggesting that it may play a role in cellular proteostasis.
Collapse
Affiliation(s)
- Marta A. Inchingolo
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aurélie Diman
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Maxime Adamczewski
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Faculté de Médecine et Pharmacie, Université Grenoble Alpes, Grenoble, France
| | - Tom Humphreys
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Pascale Jaquier-Gubler
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Joseph A. Curran
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| |
Collapse
|
35
|
Kienzle L, Bettinazzi S, Choquette T, Brunet M, Khorami HH, Jacques JF, Moreau M, Roucou X, Landry CR, Angers A, Breton S. A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics. BMC Biol 2023; 21:111. [PMID: 37198654 DOI: 10.1186/s12915-023-01609-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. RESULTS We found a downstream alternative ATG initiation codon in the + 3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. CONCLUSIONS Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.
Collapse
Affiliation(s)
- Laura Kienzle
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Stefano Bettinazzi
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Thierry Choquette
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Marie Brunet
- Service de génétique médicale, Département de pédiatrie, Université de Sherbrooke, Sherbrooke, Canada
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Canada
| | | | - Jean-François Jacques
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Mathilde Moreau
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Xavier Roucou
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, Canada
- Département de biochimie et génomique fonctionnelle, Université de Sherbrooke, Sherbrooke, Canada
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
| | - Annie Angers
- Département de sciences biologiques, Université de Montréal, Montréal, Canada
| | - Sophie Breton
- Département de sciences biologiques, Université de Montréal, Montréal, Canada.
| |
Collapse
|
36
|
Sandmann CL, Schulz JF, Ruiz-Orera J, Kirchner M, Ziehm M, Adami E, Marczenke M, Christ A, Liebe N, Greiner J, Schoenenberger A, Muecke MB, Liang N, Moritz RL, Sun Z, Deutsch EW, Gotthardt M, Mudge JM, Prensner JR, Willnow TE, Mertins P, van Heesch S, Hubner N. Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames. Mol Cell 2023; 83:994-1011.e18. [PMID: 36806354 PMCID: PMC10032668 DOI: 10.1016/j.molcel.2023.01.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/12/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023]
Abstract
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.
Collapse
Affiliation(s)
- Clara-L Sandmann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany
| | - Jana F Schulz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany
| | - Jorge Ruiz-Orera
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Marieluise Kirchner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | - Matthias Ziehm
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | - Eleonora Adami
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Maike Marczenke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Annabel Christ
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Nina Liebe
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Johannes Greiner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Aaron Schoenenberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Michael B Muecke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Ning Liang
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | | | - Zhi Sun
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Michael Gotthardt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John R Prensner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Thomas E Willnow
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | | | - Norbert Hubner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany.
| |
Collapse
|
37
|
Pueyo JI, Salazar J, Grincho C, Berni J, Towler BP, Newbury SF. Purriato is a conserved small open reading frame gene that interacts with the CASA pathway to regulate muscle homeostasis and epithelial tissue growth in Drosophila. Front Cell Dev Biol 2023; 11:1117454. [PMID: 36968202 PMCID: PMC10036370 DOI: 10.3389/fcell.2023.1117454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
Recent advances in proteogenomic techniques and bioinformatic pipelines have permitted the detection of thousands of translated small Open Reading Frames (smORFs), which contain less than 100 codons, in eukaryotic genomes. Hundreds of these actively translated smORFs display conserved sequence, structure and evolutionary signatures indicating that the translated peptides could fulfil important biological roles. Despite their abundance, only tens of smORF genes have been fully characterised; these act mainly as regulators of canonical proteins involved in essential cellular processes. Importantly, some of these smORFs display conserved functions with their mutations being associated with pathogenesis. Thus, investigating smORF roles in Drosophila will not only expand our understanding of their functions but it may have an impact in human health. Here we describe the function of a novel and essential Drosophila smORF gene named purriato (prto). prto belongs to an ancient gene family whose members have expanded throughout the Protostomia clade. prto encodes a transmembrane peptide which is localized in endo-lysosomes and perinuclear and plasma membranes. prto is dynamically expressed in mesodermal tissues and imaginal discs. Targeted prto knockdown (KD) in these organs results in changes in nuclear morphology and endo-lysosomal distributions correlating with the loss of sarcomeric homeostasis in muscles and reduction of mitosis in wing discs. Consequently, prto KD mutants display severe reduction of motility, and shorter wings. Finally, our genetic interaction experiments show that prto function is closely associated to the CASA pathway, a conserved mechanism involved in turnover of mis-folded proteins and linked to muscle dystrophies and neurodegenerative diseases. Thus, this study shows the relevance of smORFs in regulating important cellular functions and supports the systematic characterisation of this class of genes to understand their functions and evolution.
Collapse
Affiliation(s)
- Jose I. Pueyo
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jorge Salazar
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Carolina Grincho
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jimena Berni
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Benjamin P. Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sarah F. Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| |
Collapse
|
38
|
Li J, Qu X, Guan C, Luo N, Chen H, Li A, Zhuang H, Yang J, Diao H, Zeng S, Wang Q, Fan J, Jiang M, Bai X, Ye Z, Jiang X, Chen W, Nikolic-Paterson DJ, Yu X. Mitochondrial micropeptide MOXI promotes fibrotic gene transcription by translocation to the nucleus and bridging N-acetyltransferase 14 with transcription factor c-Jun. Kidney Int 2023; 103:886-902. [PMID: 36804379 DOI: 10.1016/j.kint.2023.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/04/2023] [Accepted: 01/20/2023] [Indexed: 02/17/2023]
Abstract
Progressive fibrosis is a hallmark of chronic kidney disease, but we lack effective treatments to halt this destructive process. Micropeptides (peptides of no more than 100 amino acids) encoded by small open reading frames represent a new class of eukaryotic regulators. Here, we describe that the micropeptide regulator of β-oxidation (MOXI) regulates 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 translocated 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.
Collapse
Affiliation(s)
- Jinhua Li
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China; Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia; Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Xinli Qu
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Chengnong Guan
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Ning Luo
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Huiting Chen
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Andy Li
- Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia
| | - Hongjie Zhuang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiayi Yang
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Hui Diao
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Shuhan Zeng
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qing Wang
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Jinjin Fan
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Mengjie Jiang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Bai
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhiming Ye
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoyun Jiang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - David J Nikolic-Paterson
- Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia
| | - Xueqing Yu
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China.
| |
Collapse
|
39
|
Treichel AJ, Bazzini AA. Casting CRISPR-Cas13d to fish for microprotein functions in animal development. iScience 2022; 25:105547. [PMID: 36444300 PMCID: PMC9700322 DOI: 10.1016/j.isci.2022.105547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Protein coding genes were originally identified with sequence-based definitions that included a 100-codon cutoff to avoid annotating irrelevant open reading frames. However, many active proteins contain less than 100 amino acids. Indeed, functional genetics, ribosome profiling, and proteomic profiling have identified many short, translated open reading frames, including those with biologically active peptide products (microproteins). Yet, functions for most of these peptide products remain unknown. Because microproteins often act as key signals or fine-tune processes, animal development has already revealed functions for a handful of microproteins and provides an ideal context to uncover additional microprotein functions. However, many mRNAs during early development are maternally provided and hinder targeted mutagenesis approaches to characterize developmental microprotein functions. The recently established, RNA-targeting CRISPR-Cas13d system in zebrafish overcomes this barrier and produces potent knockdown of targeted mRNA, including maternally provided mRNA, and enables flexible, efficient interrogation of microprotein functions in animal development.
Collapse
Affiliation(s)
| | - Ariel Alejandro Bazzini
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
40
|
MacPherson RA, Shankar V, Sunkara LT, Hannah RC, Campbell MR, Anholt RRH, Mackay TFC. Pleiotropic fitness effects of the lncRNA Uhg4 in Drosophila melanogaster. BMC Genomics 2022; 23:781. [PMID: 36451091 PMCID: PMC9710044 DOI: 10.1186/s12864-022-08972-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are a diverse class of RNAs that are critical for gene regulation, DNA repair, and splicing, and have been implicated in development, stress response, and cancer. However, the functions of many lncRNAs remain unknown. In Drosophila melanogaster, U snoRNA host gene 4 (Uhg4) encodes an antisense long noncoding RNA that is host to seven small nucleolar RNAs (snoRNAs). Uhg4 is expressed ubiquitously during development and in all adult tissues, with maximal expression in ovaries; however, it has no annotated function(s). RESULTS We used CRISPR-Cas9 germline gene editing to generate multiple deletions spanning the promoter region and first exon of Uhg4. Females showed arrested egg development and both males and females were sterile. In addition, Uhg4 deletion mutants showed delayed development and decreased viability, and changes in sleep and responses to stress. Whole-genome RNA sequencing of Uhg4 deletion flies and their controls identified co-regulated genes and genetic interaction networks associated with Uhg4. Gene ontology analyses highlighted a broad spectrum of biological processes, including regulation of transcription and translation, morphogenesis, and stress response. CONCLUSION Uhg4 is a lncRNA essential for reproduction with pleiotropic effects on multiple fitness traits.
Collapse
Affiliation(s)
- Rebecca A MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Lakshmi T Sunkara
- Present adress: Clemson Veterinary Diagnostic Center, Livestock Poultry Health, Clemson University, 500 Clemson Road, Columbia, SC, 29229, USA
| | - Rachel C Hannah
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Marion R Campbell
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
| | - Trudy F C Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
| |
Collapse
|
41
|
Bosch JA, Ugur B, Pichardo-Casas I, Rabasco J, Escobedo F, Zuo Z, Brown B, Celniker S, Sinclair DA, Bellen HJ, Perrimon N. Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III in Drosophila. eLife 2022; 11:e82709. [PMID: 36346220 PMCID: PMC9681215 DOI: 10.7554/elife.82709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/01/2022] [Indexed: 11/10/2022] Open
Abstract
Naturally produced peptides (<100 amino acids) are important regulators of physiology, development, and metabolism. Recent studies have predicted that thousands of peptides may be translated from transcripts containing small open-reading frames (smORFs). Here, we describe two peptides in Drosophila encoded by conserved smORFs, Sloth1 and Sloth2. These peptides are translated from the same bicistronic transcript and share sequence similarities, suggesting that they encode paralogs. Yet, Sloth1 and Sloth2 are not functionally redundant, and loss of either peptide causes animal lethality, reduced neuronal function, impaired mitochondrial function, and neurodegeneration. We provide evidence that Sloth1/2 are highly expressed in neurons, imported to mitochondria, and regulate mitochondrial complex III assembly. These results suggest that phenotypic analysis of smORF genes in Drosophila can provide a wealth of information on the biological functions of this poorly characterized class of genes.
Collapse
Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnick Institute, Harvard Medical SchoolBostonUnited States
| | - Berrak Ugur
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Israel Pichardo-Casas
- Department of Genetics, Blavatnick Institute, Harvard Medical SchoolBostonUnited States
| | - Jordan Rabasco
- Department of Genetics, Blavatnick Institute, Harvard Medical SchoolBostonUnited States
| | - Felipe Escobedo
- Department of Genetics, Blavatnick Institute, Harvard Medical SchoolBostonUnited States
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Ben Brown
- Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Susan Celniker
- Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - David A Sinclair
- Department of Genetics, Blavatnick Institute, Harvard Medical SchoolBostonUnited States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Howard Hughes Medical InstituteHoustonUnited States
| | - Norbert Perrimon
- Department of Genetics, Blavatnick Institute, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical InstituteHoustonUnited States
| |
Collapse
|
42
|
Zheng X, Xiang M. Mitochondrion-located peptides and their pleiotropic physiological functions. FEBS J 2022; 289:6919-6935. [PMID: 35599630 DOI: 10.1111/febs.16532] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 01/13/2023]
Abstract
With the development of advanced technologies, many small open reading frames (sORFs) have been found to be translated into micropeptides. Interestingly, a considerable proportion of micropeptides are located in mitochondria, which are designated here as mitochondrion-located peptides (MLPs). These MLPs often contain a transmembrane domain and show a high degree of conservation across species. They usually act as co-factors of large proteins and play regulatory roles in mitochondria such as electron transport in the respiratory chain, reactive oxygen species (ROS) production, metabolic homeostasis, and so on. Deficiency of MLPs disturbs diverse physiological processes including immunity, differentiation, and metabolism both in vivo and in vitro. These findings reveal crucial functions for MLPs and provide fresh insights into diverse mitochondrion-associated biological processes and diseases.
Collapse
Affiliation(s)
- Xintong Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
43
|
Translation and natural selection of micropeptides from long non-canonical RNAs. Nat Commun 2022; 13:6515. [PMID: 36316320 PMCID: PMC9622821 DOI: 10.1038/s41467-022-34094-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but lacking canonical coding sequences. Apparently unable to produce peptides, lncRNA function seems to rely only on RNA expression, sequence and structure. Here, we exhaustively detect in-vivo translation of small open reading frames (small ORFs) within lncRNAs using Ribosomal profiling during Drosophila melanogaster embryogenesis. We show that around 30% of lncRNAs contain small ORFs engaged by ribosomes, leading to regulated translation of 100 to 300 micropeptides. We identify lncRNA features that favour translation, such as cistronicity, Kozak sequences, and conservation. For the latter, we develop a bioinformatics pipeline to detect small ORF homologues, and reveal evidence of natural selection favouring the conservation of micropeptide sequence and function across evolution. Our results expand the repertoire of lncRNA biochemical functions, and suggest that lncRNAs give rise to novel coding genes throughout evolution. Since most lncRNAs contain small ORFs with as yet unknown translation potential, we propose to rename them "long non-canonical RNAs".
Collapse
|
44
|
Tan HW, Xu YM, Liang ZL, Cai NL, Wu YY, Lau ATY. Single-gene knockout-coupled omics analysis identifies C9orf85 and CXorf38 as two uncharacterized human proteins associated with ZIP8 malfunction. Front Mol Biosci 2022; 9:991308. [PMID: 36330220 PMCID: PMC9623088 DOI: 10.3389/fmolb.2022.991308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/13/2022] [Indexed: 02/05/2023] Open
Abstract
Human transmembrane protein metal cation symporter ZIP8 (SLC39A8) is a member of the solute carrier gene family responsible for intracellular transportation of essential micronutrients, including manganese, selenium, and zinc. Previously, we established a ZIP8-knockout (KO) human cell model using the CRISPR/Cas9 system and explored how the expression of ZIP8 could possibly contribute to a wide range of human diseases. To further assess the biophysiological role of ZIP8, in the current study, we employed isobaric tags for relative and absolute quantitation (iTRAQ) and detected the changes of the proteome in ZIP8-KO cells (proteomic data are available via ProteomeXchange with identifier PXD036680). A total of 286 differentially expressed proteins (206 downregulated and 80 upregulated proteins) were detected in the ZIP8-KO cell model, and subsequent bioinformatics analyses (GO, KEGG, KOG, and PPI) were performed on these proteins. Interestingly, four "uncharacterized" proteins (proteins with unknown biological function) were identified in the differentially expressed proteins: C1orf198, C9orf85, C17orf75, and CXorf38-all of which were under-expressed in the ZIP8-KO cells. Notably, C9orf85 and CXorf38 were amongst the top-10 most downregulated proteins, and their expressions could be selectively induced by essential micronutrients. Furthermore, clinical-based bioinformatic analysis indicated that positive correlations between the gene expressions of ZIP8 and C9orf85 or CXorf38 were observed in multiple cancer types. Overall, this study reveals the proteomic landscape of cells with impaired ZIP8 and uncovers the potential relationships between essential micronutrients and uncharacterized proteins C9orf85 and CXorf38. The differentially expressed proteins identified in ZIP8-KO cells could be the potential targets for diagnosing and/or treating human ZIP8-associated diseases, including but not limited to malnutrition, viral infection, and cancers.
Collapse
Affiliation(s)
- Heng Wee Tan
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, China
| | | | | | | | | | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, China
| |
Collapse
|
45
|
Bak JJ, Aguayo-Ortiz R, Rathod N, Primeau JO, Khan MB, Robia SL, Lemieux MJ, Espinoza-Fonseca LM, Young HS. Primitive Phospholamban- and Sarcolipin-like Peptides Inhibit the Sarcoplasmic Reticulum Calcium Pump SERCA. Biochemistry 2022; 61:1419-1430. [PMID: 35771007 PMCID: PMC10588654 DOI: 10.1021/acs.biochem.2c00246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Intracellular calcium signaling is essential for all kingdoms of life. An important part of this process is the sarco-endoplasmic reticulum Ca2+-ATPase (SERCA), which maintains the low cytosolic calcium levels required for intracellular calcium homeostasis. In higher organisms, SERCA is regulated by a series of tissue-specific transmembrane subunits such as phospholamban in cardiac muscles and sarcolipin in skeletal muscles. These regulatory axes are so important for muscle contractility that SERCA, phospholamban, and sarcolipin are practically invariant across mammalian species. With the recent discovery of the arthropod sarcolambans, the family of calcium pump regulatory subunits appears to span more than 550 million years of evolutionary divergence from arthropods to humans. This evolutionary divergence is reflected in the peptide sequences, which vary enormously from one another and only vaguely resemble phospholamban and sarcolipin. The discovery of the sarcolambans allowed us to address two questions. How much sequence variation is tolerated in the regulation of mammalian SERCA activity by the transmembrane peptides? Do divergent peptide sequences mimic phospholamban or sarcolipin in their regulatory activities despite limited sequence similarity? We expressed and purified recombinant sarcolamban peptides from three different arthropods. The peptides were coreconstituted into proteoliposomes with mammalian SERCA1a and the effect of each peptide on the apparent calcium affinity and maximal activity of SERCA was measured. All three peptides were superinhibitors of SERCA, exhibiting either phospholamban-like or sarcolipin-like characteristics. Molecular modeling, protein-protein docking, and molecular dynamics simulations revealed novel features of the divergent peptides and their SERCA regulatory properties.
Collapse
Affiliation(s)
- Jessi J. Bak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Rodrigo Aguayo-Ortiz
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nishadh Rathod
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Joseph O. Primeau
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Seth L. Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - M. Joanne Lemieux
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - L. Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Howard S. Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| |
Collapse
|
46
|
Anapindi KDB, Romanova EV, Checco JW, Sweedler JV. Mass Spectrometry Approaches Empowering Neuropeptide Discovery and Therapeutics. Pharmacol Rev 2022; 74:662-679. [PMID: 35710134 PMCID: PMC9553102 DOI: 10.1124/pharmrev.121.000423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The discovery of insulin in the early 1900s ushered in the era of research related to peptides acting as hormones and neuromodulators, among other regulatory roles. These essential gene products are found in all organisms, from the most primitive to the most evolved, and carry important biologic information that coordinates complex physiology and behavior; their misregulation has been implicated in a variety of diseases. The evolutionary origins of at least 30 neuropeptide signaling systems have been traced to the common ancestor of protostomes and deuterostomes. With the use of relevant animal models and modern technologies, we can gain mechanistic insight into orthologous and paralogous endogenous peptides and translate that knowledge into medically relevant insights and new treatments. Groundbreaking advances in medicine and basic science influence how signaling peptides are defined today. The precise mechanistic pathways for over 100 endogenous peptides in mammals are now known and have laid the foundation for multiple drug development pipelines. Peptide biologics have become valuable drugs due to their unique specificity and biologic activity, lack of toxic metabolites, and minimal undesirable interactions. This review outlines modern technologies that enable neuropeptide discovery and characterization, and highlights lessons from nature made possible by neuropeptide research in relevant animal models that is being adopted by the pharmaceutical industry. We conclude with a brief overview of approaches/strategies for effective development of peptides as drugs. SIGNIFICANCE STATEMENT: Neuropeptides, an important class of cell-cell signaling molecules, are involved in maintaining a range of physiological functions. Since the discovery of insulin's activity, over 100 bioactive peptides and peptide analogs have been used as therapeutics. Because these are complex molecules not easily predicted from a genome and their activity can change with subtle chemical modifications, mass spectrometry (MS) has significantly empowered peptide discovery and characterization. This review highlights contributions of MS-based research towards the development of therapeutic peptides.
Collapse
Affiliation(s)
- Krishna D B Anapindi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - James W Checco
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| |
Collapse
|
47
|
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Standardized annotation of translated open reading frames. Nat Biotechnol 2022; 40:994-999. [PMID: 35831657 PMCID: PMC9757701 DOI: 10.1038/s41587-022-01369-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - John R Prensner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
| | - Marie A Brunet
- Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Ferriol Calvet
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Jose Manuel Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michele Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas F Martinez
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Yucheng T Yang
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- LeedsOmics, University of Leeds, Leeds, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Elspeth Bruford
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Maria Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lorenzo Calviello
- Functional Genomics Centre, Human Technopole, Milan, Italy
- Computational Biology Centre, Human Technopole, Milan, Italy
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Juan Pablo Couso
- Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mark Gerstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Gerben Menschaert
- Biobix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | | | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jonathan S Weissman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | |
Collapse
|
48
|
Kragness S, Clark Z, Mullin A, Guidry J, Earls LR. An Rtn4/Nogo-A-interacting micropeptide modulates synaptic plasticity with age. PLoS One 2022; 17:e0269404. [PMID: 35771867 PMCID: PMC9246188 DOI: 10.1371/journal.pone.0269404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
Micropeptides, encoded from small open reading frames of 300 nucleotides or less, are hidden throughout mammalian genomes, though few functional studies of micropeptides in the brain are published. Here, we describe a micropeptide known as the Plasticity–Associated Neural Transcript Short (Pants), located in the 22q11.2 region of the human genome, the microdeletion of which conveys a high risk for schizophrenia. Our data show that Pants is upregulated in early adulthood in the mossy fiber circuit of the hippocampus, where it exerts a powerful negative effect on long-term potentiation (LTP). Further, we find that Pants is secreted from neurons, where it associates with synapses but is rapidly degraded with stimulation. Pants dynamically interacts with Rtn4/Nogo-A, a well-studied regulator of adult plasticity. Pants interaction with Nogo-A augments its influence over postsynaptic AMPA receptor clustering, thus gating plasticity at adult synapses. This work shows that neural micropeptides can act as architectural modules that increase the functional diversity of the known proteome.
Collapse
Affiliation(s)
- S. Kragness
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States of America
| | - Z. Clark
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States of America
| | - A. Mullin
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States of America
- Tulane University Transgenic Core Facility, New Orleans, LA, United States of America
| | - J. Guidry
- Department of Biochemistry and Molecular Biology, LSU School of Medicine and Health Sciences Center, New Orleans, LA, United States of America
- The Proteomics Core Facility, LSUHSC, New Orleans, LA, United States of America
| | - L. R. Earls
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States of America
- * E-mail:
| |
Collapse
|
49
|
Camilleri-Robles C, Amador R, Klein CC, Guigó R, Corominas M, Ruiz-Romero M. Genomic and functional conservation of lncRNAs: lessons from flies. Mamm Genome 2022; 33:328-342. [PMID: 35098341 PMCID: PMC9114055 DOI: 10.1007/s00335-021-09939-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022]
Abstract
Over the last decade, the increasing interest in long non-coding RNAs (lncRNAs) has led to the discovery of these transcripts in multiple organisms. LncRNAs tend to be specifically, and often lowly, expressed in certain tissues, cell types and biological contexts. Although lncRNAs participate in the regulation of a wide variety of biological processes, including development and disease, most of their functions and mechanisms of action remain unknown. Poor conservation of the DNA sequences encoding for these transcripts makes the identification of lncRNAs orthologues among different species very challenging, especially between evolutionarily distant species such as flies and humans or mice. However, the functions of lncRNAs are unexpectedly preserved among different species supporting the idea that conservation occurs beyond DNA sequences and reinforcing the potential of characterising lncRNAs in animal models. In this review, we describe the features and roles of lncRNAs in the fruit fly Drosophila melanogaster, focusing on genomic and functional comparisons with human and mouse lncRNAs. We also discuss the current state of advances and limitations in the study of lncRNA conservation and future perspectives.
Collapse
Affiliation(s)
- Carlos Camilleri-Robles
- Departament de Genètica, Microbiologia I Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Raziel Amador
- Departament de Genètica, Microbiologia I Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Cecilia C Klein
- Departament de Genètica, Microbiologia I Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Montserrat Corominas
- Departament de Genètica, Microbiologia I Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marina Ruiz-Romero
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain.
| |
Collapse
|
50
|
Zhou H, Lou F, Bai J, Sun Y, Cai W, Sun L, Xu Z, Liu Z, Zhang L, Yin Q, Zhang J, Gao Y, Wang Z, Niu L, Cai X, Deng S, Wang H, Xia L, Ginhoux F, Li Q, Wang H. A peptide encoded by pri-miRNA-31 represses autoimmunity by promoting T reg differentiation. EMBO Rep 2022; 23:e53475. [PMID: 35343645 PMCID: PMC9066071 DOI: 10.15252/embr.202153475] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/29/2022] Open
Abstract
Recent evidence has revealed that small polypeptides (containing fewer than 100 amino acids) can be translated from noncoding RNAs (ncRNAs), which are usually defined as RNA molecules that do not encode proteins. However, studies on functional products translated from primary transcripts of microRNA (pri-miRNA) are quite limited. Here, we describe a peptide termed miPEP31 that is encoded by pri-miRNA-31. miPEP31 is highly expressed in Foxp3+ regulatory T cells (Tregs ) and significantly promotes the differentiation of Tregs without affecting their inhibitory ability. Our results show that miPEP31 is a cell-penetrating peptide both in vitro and in vivo. miPEP31 downregulates miR-31 expression, enhances peripheral Treg induction, and dramatically suppresses experimental autoimmune encephalomyelitis. Mechanistically, we show that miPEP31 acts as a transcriptional repressor inhibiting the expression of miRNA-31, a negative regulator of Tregs . Our results reveal an indispensable role of miPEP31 in maintaining immune homeostasis by promoting Treg differentiation and also present a potential therapeutic peptide for modulating miRNA expression and treating autoimmune diseases.
Collapse
Affiliation(s)
- Hong Zhou
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fangzhou Lou
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Bai
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Sun
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Cai
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Libo Sun
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenyao Xu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaoyuan Liu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingyun Zhang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianqian Yin
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junxun Zhang
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanyuan Gao
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhikai Wang
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liman Niu
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojie Cai
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siyu Deng
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Wang
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Xia
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Florent Ginhoux
- Shanghai Institute of Immunology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Qun Li
- The Department of Cardiovascular Medicine, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Ruijin Hospital, Shanghai Institute of Hypertension, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Honglin Wang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|