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Daisy Precilla S, Biswas I, Anitha TS, Agieshkumar B. Microproteins unveiling new dimensions in cancer. Funct Integr Genomics 2024; 24:152. [PMID: 39223429 DOI: 10.1007/s10142-024-01426-8] [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: 06/17/2024] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
In the complex landscape of cancer biology, the discovery of microproteins has triggered a paradigm shift, thereby, challenging the conventional conceptions of gene regulation. Though overlooked for years, these entities encoded by the small open reading frames (100-150 codons), have a significant impact on various cellular processes. As precision medicine pioneers delve deeper into the genome and proteome, microproteins have come into the limelight. Typically characterized by a single protein domain that directly binds to the target protein complex and regulates their assembly, these microproteins have been shown to play a key role in fundamental biological processes such as RNA processing, DNA repair, and metabolism regulation. Techniques for identification and characterization, such as ribosome profiling and proteogenomic approaches, have unraveled unique mechanisms by which these microproteins regulate cell signaling or pathological processes in most diseases including cancer. However, the functional relevance of these microproteins in cancer remains unclear. In this context, the current review aims to "rethink the essence of these genes" and explore "how these hidden players-microproteins orchestrate the signaling cascades of cancer, both as accelerators and brakes.".
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Affiliation(s)
- S Daisy Precilla
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth, Puducherry, 607 402, India.
| | - Indrani Biswas
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth, Puducherry, 607 402, India
| | - T S Anitha
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, 605 014, India
| | - B Agieshkumar
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth, Puducherry, 607 402, India
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Chen HX, Ma YZ, Xie PP, Huang JY, Li LQ, Zhang W, Zhu Y, Zhuang SM, Lin YF. Micropeptide MPM regulates cardiomyocyte proliferation and heart growth via the AKT pathway. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119820. [PMID: 39163918 DOI: 10.1016/j.bbamcr.2024.119820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/26/2024] [Accepted: 08/14/2024] [Indexed: 08/22/2024]
Abstract
The role of micropeptide in cardiomyocyte proliferation remains unknown. We found that MPM (micropeptide in mitochondria) was highly expressed in cardiomyocytes. Compared to MPM+/+ mice, MPM knockout (MPM-/-) mice exhibited reduction in left ventricular (LV) mass, myocardial thickness and LV fractional shortening. RNA-sequencing analysis in H9c2, a rat cardiomyocyte cell line, identified downregulation of cell cycle-promoting genes as the most significant alteration in MPM-silencing cells. Consistently, gain- and loss-of-function analyses in H9c2 cells revealed that cardiomyocyte proliferation was repressed by silencing MPM but was promoted by overexpressing MPM. Moreover, the cardiomyocytes in the hearts of MPM-/- mice displayed reduced proliferation rates. Mechanism investigations disclosed that MPM is crucial for AKT activation in cardiomyocytes. We also identified an interaction between MPM and PTPMT1, and found that silencing PTPMT1 attenuated the effect of MPM in activating the AKT pathway, whereas inhibition of the AKT pathway abrogated the role of MPM in promoting cardiomyocyte proliferation. Collectively, these results indicate that MPM may promote cardiomyocyte proliferation and thus heart growth by interacting with PTPMT1 to activate the AKT pathway. Our findings identify the novel function and regulatory network of MPM and highlight the importance of micropeptides in cardiomyocyte proliferation and heart growth.
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Affiliation(s)
- Hua-Xing Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yan-Zhen Ma
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Peng-Peng Xie
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jie-Yi Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Lan-Qi Li
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wei Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Ying Zhu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shi-Mei Zhuang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China; Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, PR China.
| | - Yi-Fang Lin
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou 510275, PR China; Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, PR China.
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Witmer NH, McLendon JM, Stein CS, Yoon JY, Berezhnaya E, Elrod JW, London BL, Boudreau RL. Upstream alternative polyadenylation in SCN5A produces a short transcript isoform encoding a mitochondria-localized NaV1.5 N-terminal fragment that influences cardiomyocyte respiration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607406. [PMID: 39211120 PMCID: PMC11360925 DOI: 10.1101/2024.08.09.607406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
SCN5A encodes the cardiac voltage-gated Na+ channel, NaV1.5, that initiates action potentials. SCN5A gene variants cause arrhythmias and increased heart failure risk. Mechanisms controlling NaV1.5 expression and activity are not fully understood. We recently found a well-conserved alternative polyadenylation (APA) signal downstream of the first SCN5A coding exon. This yields a SCN5A-short transcript isoform expressed in several species (e.g. human, pig, and cat), though rodents lack this upstream APA. Reanalysis of transcriptome-wide cardiac APA-seq and mRNA-seq data shows reductions in both upstream APA usage and short/full-length SCN5A mRNA ratios in failing hearts. Knock-in of the human SCN5A APA sequence into mice is sufficient to enable expression of SCN5A -short transcript, while significantly decreasing expression of full-length SCN5A mRNA. Notably, SCN5A -short transcript encodes a novel protein (NaV1.5-NT), composed of an N-terminus identical to NaV1.5 and a unique C-terminus derived from intronic sequence. AAV9 constructs were able to achieve stable NaV1.5-NT expression in mouse hearts, and western blot of human heart tissues showed bands co-migrating with NaV1.5-NT transgene-derived bands. NaV1.5-NT is predicted to contain a mitochondrial targeting sequence and localizes to mitochondria in cultured cardiomyocytes and in mouse hearts. NaV1.5-NT expression in cardiomyocytes led to elevations in basal oxygen consumption rate, ATP production, and mitochondrial ROS, while depleting NADH supply. Native PAGE analyses of mitochondria lysates revealed that NaV1.5-NT expression resulted in increased levels of disassembled complex V subunits and accumulation of complex I-containing supercomplexes. Overall, we discovered that APA-mediated regulation of SCN5A produces a short transcript encoding NaV1.5-NT. Our data support that NaV1.5-NT plays a multifaceted role in influencing mitochondrial physiology: 1) by increasing basal respiration likely through promoting complex V conformations that enhance proton leak, and 2) by increasing overall respiratory efficiency and NADH consumption by enhancing formation and/or stability of complex I-containing respiratory supercomplexes, though the specific molecular mechanisms underlying each of these remain unresolved.
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Wang Z, Jia X, Sun W, Wang M, Yuan Q, Xu T, Liu Y, Chen Z, Huang M, Ji N, Zhang M. A micropeptide TREMP encoded by lincR-PPP2R5C promotes Th2 cell differentiation by interacting with PYCR1 in allergic airway inflammation. Allergol Int 2024:S1323-8930(24)00048-0. [PMID: 39025723 DOI: 10.1016/j.alit.2024.04.004] [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: 12/13/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Allergic asthma is largely dominated by Th2 lymphocytes. Micropeptides in Th2 cells and asthma remain unmasked. Here, we aimed to demonstrate a micropeptide, T-cell regulatory micropeptide (TREMP), in Th2 cell differentiation in asthma. METHODS TREMP translated from lincR-PPP2R5C was validated using Western blotting and mass spectrometry. TREMP knockout mice were generated using CRISPR/Cas9. Coimmunoprecipitation revealed that TREMP targeted pyrroline-5-carboxylate reductase 1 (PYCR1), which was further explored in vitro and in vivo. The levels of TREMP and PYCR1 in Th2 cells from clinical samples were determined by flow cytometry. RESULTS TREMP, encoded by lincR-PPP2R5C, was in the mitochondrion. The lentivirus encoding TREMP promoted Th2 cell differentiation. In contrast, Th2 differentiation was suppressed in TREMP-/- CD4+ T cells. In the HDM-induced model of allergic airway inflammation, TREMP was increased in pulmonary tissues. Allergic airway inflammation was relieved in TREMP-/- mice treated with HDM. Mechanistically, TREMP interacted with PYCR1, which regulated Th2 differentiation via glycolysis. Glycolysis was decreased in Th2 cells from TREMP-/- mice and PYCR1-/- mice. Similar to TREMP-/- mice, allergic airway inflammation was mitigated in HDM-challenged PYCR1-/- mice. Moreover, we measured TREMP and PYCR1 in asthma patients. And we found that, compared with those in healthy controls, the levels of TREMP and PYCR1 in Th2 cells were significantly increased in asthmatic patients. CONCLUSIONS The micropeptide TREMP encoded by lincR-PPP2R5C promoted Th2 differentiation in allergic airway inflammation by interacting with PYCR1 and enhancing glycolysis. Our findings highlight the importance of neglected micropeptides from noncoding RNAs in allergic diseases.
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Affiliation(s)
- Zhengxia Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xinyu Jia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Sun
- Department of Respiratory and Critical Care Medicine, Xishan People's Hospital of Wuxi City, Wuxi Branch of Zhongda Hospital Affiliate to Southeast University, Wuxi, China
| | - Min Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Yuan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tingting Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanan Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Zhongqi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mao Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Ningfei Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Mingshun Zhang
- NHC Key Laboratory of Antibody Technique, Department of Immunology, Nanjing Medical University, Nanjing, China.
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Peng M, Zhou Y, Wan C. Identification of phosphorylated small ORF-encoded peptides in Hep3B cells by LC/MS/MS. J Proteomics 2024; 303:105214. [PMID: 38823442 DOI: 10.1016/j.jprot.2024.105214] [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: 02/20/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Small ORF-encoded peptides (SEPs) are a class of low molecular weight proteins and peptides comprising <100 amino acids with important functions in various life activities. Although the sequence length is short, SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. In this work, we enriched phosphopeptides with IMAC and TiO2 materials and analyzed the phosphorylated SEPs in Hep3B cells. A total of 24 phosphorylated SEPs were identified, and 11 SEPs were coded by ncRNA. For the sequence analysis, we found that the general characteristics of phosphorylated SEPs are roughly the same as canonical proteins. Besides, two phosphorylation SEPs have the Stathmin family signature 2 motif, which can regulate the microtubule cytoskeleton. Some SEPs have domains or signal peptides, indicating their specific functions and subcellular locations. Kinase network analysis found a small number of kinases that may be a clue to the specific functions of some SEPs. However, only one-fifth of the predicted phosphorylation sites were identified by LC/MS/MS, indicating that many SEP PTMs are hidden in the dark, waiting to be uncovered and verified. This study helps expand our understanding of SEP and provides information for further SEP function investigation. SIGNIFICANCE: Small ORF-encoded peptides (SEPs) are important in various life activities. Although the sequence length is short (<100AA), SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. We enriched phosphopeptides and analyzed the phosphorylated SEPs in Hep3B cells. That is the first time to explore the PTM of SPEs systematically. Kinase network analysis found a small number of kinases that may be a clue to the specific functions of SEPs. More SEP PTMs are hidden in the dark and waiting to be uncovered and verified. This study helps expand our understanding of SEP and provides information for further SEP function investigation.
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Affiliation(s)
- Mingbo Peng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yutian Zhou
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.
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Linzer CR, Stein CS, Witmer NH, Xu Z, Schnicker NJ, Boudreau RL. Mitoregulin self-associates to form likely homo-oligomeric pore-like structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.601956. [PMID: 39026732 PMCID: PMC11257578 DOI: 10.1101/2024.07.10.601956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
We and others previously found that a misannotated long noncoding RNA encodes for a conserved mitochondrial transmembrane microprotein named Mitoregulin (Mtln). Beyond an established role for Mtln in lipid metabolism, Mtln has also been shown to more broadly influence mitochondria, boosting respiratory efficiency and Ca 2+ retention capacity, while lowering ROS, yet the underlying mechanisms remain unresolved. Prior studies have identified possible Mtln protein interaction partners; however, a lack of consensus persists, and no claims have been made about Mtln's structure. We previously noted two key published observations that seemingly remained overlooked: 1) endogenous Mtln co-immunoprecipitates with epitope-tagged Mtln at high efficiency, and 2) Mtln primarily exists in a ∼66 kDa complex. To investigate if Mtln may self-oligomerize into higher-order complexes, we performed co-immunoprecipitation, protein modeling simulations, and native gel assessments of Mtln-containing complexes in cells and tissues, as well as tested whether synthetic Mtln protein itself forms oligomeric complexes. Our combined results provide strong support that Mtln self-associates and likely forms a hexameric pore-like structure.
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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] [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.
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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.
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Wen K, Chen X, Gu J, Chen Z, Wang Z. Beyond traditional translation: ncRNA derived peptides as modulators of tumor behaviors. J Biomed Sci 2024; 31:63. [PMID: 38877495 PMCID: PMC11177406 DOI: 10.1186/s12929-024-01047-0] [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: 11/29/2023] [Accepted: 05/24/2024] [Indexed: 06/16/2024] Open
Abstract
Within the intricate tapestry of molecular research, noncoding RNAs (ncRNAs) were historically overshadowed by a pervasive presumption of their inability to encode proteins or peptides. However, groundbreaking revelations have challenged this notion, unveiling select ncRNAs that surprisingly encode peptides specifically those nearing a succinct 100 amino acids. At the forefront of this epiphany stand lncRNAs and circRNAs, distinctively characterized by their embedded small open reading frames (sORFs). Increasing evidence has revealed different functions and mechanisms of peptides/proteins encoded by ncRNAs in cancer, including promotion or inhibition of cancer cell proliferation, cellular metabolism (glucose metabolism and lipid metabolism), and promotion or concerted metastasis of cancer cells. The discoveries not only accentuate the depth of ncRNA functionality but also open novel avenues for oncological research and therapeutic innovations. The main difficulties in the study of these ncRNA-derived peptides hinge crucially on precise peptide detection and sORFs identification. Here, we illuminate cutting-edge methodologies, essential instrumentation, and dedicated databases tailored for unearthing sORFs and peptides. In addition, we also conclude the potential of clinical applications in cancer therapy.
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Affiliation(s)
- Kang Wen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Jingyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Zhenyao Chen
- Department of Respiratory Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P.R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China.
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Stein CS, Zhang X, Witmer NH, Pennington ER, Shaikh SR, Boudreau RL. Mitoregulin supports mitochondrial membrane integrity and protects against cardiac ischemia-reperfusion injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596875. [PMID: 38853979 PMCID: PMC11160723 DOI: 10.1101/2024.05.31.596875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
We and others discovered a highly-conserved mitochondrial transmembrane microprotein, named Mitoregulin (Mtln), that supports lipid metabolism. We reported that Mtln strongly binds cardiolipin (CL), increases mitochondrial respiration and Ca 2+ retention capacities, and reduces reactive oxygen species (ROS). Here we extend our observation of Mtln-CL binding and examine Mtln influence on cristae structure and mitochondrial membrane integrity during stress. We demonstrate that mitochondria from constitutive- and inducible Mtln-knockout (KO) mice are susceptible to membrane freeze-damage and that this can be rescued by acute Mtln re-expression. In mitochondrial-simulated lipid monolayers, we show that synthetic Mtln decreases lipid packing and monolayer elasticity. Lipidomics revealed that Mtln-KO heart tissues show broad decreases in 22:6-containing lipids and increased cardiolipin damage/remodeling. Lastly, we demonstrate that Mtln-KO mice suffer worse myocardial ischemia-reperfusion injury, hinting at a translationally-relevant role for Mtln in cardioprotection. Our work supports a model in which Mtln binds cardiolipin and stabilizes mitochondrial membranes to broadly influence diverse mitochondrial functions, including lipid metabolism, while also protecting against stress.
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Tong G, Hah N, Martinez TF. Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq. Brief Bioinform 2024; 25:bbae268. [PMID: 38842510 PMCID: PMC11155197 DOI: 10.1093/bib/bbae268] [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: 01/05/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024] Open
Abstract
Accurate and comprehensive annotation of microprotein-coding small open reading frames (smORFs) is critical to our understanding of normal physiology and disease. Empirical identification of translated smORFs is carried out primarily using ribosome profiling (Ribo-seq). While effective, published Ribo-seq datasets can vary drastically in quality and different analysis tools are frequently employed. Here, we examine the impact of these factors on identifying translated smORFs. We compared five commonly used software tools that assess open reading frame translation from Ribo-seq (RibORFv0.1, RibORFv1.0, RiboCode, ORFquant, and Ribo-TISH) and found surprisingly low agreement across all tools. Only ~2% of smORFs were called translated by all five tools, and ~15% by three or more tools when assessing the same high-resolution Ribo-seq dataset. For larger annotated genes, the same analysis showed ~74% agreement across all five tools. We also found that some tools are strongly biased against low-resolution Ribo-seq data, while others are more tolerant. Analyzing Ribo-seq coverage revealed that smORFs detected by more than one tool tend to have higher translation levels and higher fractions of in-frame reads, consistent with what was observed for annotated genes. Together these results support employing multiple tools to identify the most confident microprotein-coding smORFs and choosing the tools based on the quality of the dataset and the planned downstream characterization experiments of the predicted smORFs.
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Affiliation(s)
- Gregory Tong
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, United States
| | - Nasun Hah
- Chapman Charitable Foundations Genomic Sequencing Core, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Thomas F Martinez
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, United States
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, United States
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92617, United States
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11
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Duffy EE, Assad EG, Kalish BT, Greenberg ME. Small but mighty: the rise of microprotein biology in neuroscience. Front Mol Neurosci 2024; 17:1386219. [PMID: 38807924 PMCID: PMC11130481 DOI: 10.3389/fnmol.2024.1386219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
The mammalian central nervous system coordinates a network of signaling pathways and cellular interactions, which enable a myriad of complex cognitive and physiological functions. While traditional efforts to understand the molecular basis of brain function have focused on well-characterized proteins, recent advances in high-throughput translatome profiling have revealed a staggering number of proteins translated from non-canonical open reading frames (ncORFs) such as 5' and 3' untranslated regions of annotated proteins, out-of-frame internal ORFs, and previously annotated non-coding RNAs. Of note, microproteins < 100 amino acids (AA) that are translated from such ncORFs have often been neglected due to computational and biochemical challenges. Thousands of putative microproteins have been identified in cell lines and tissues including the brain, with some serving critical biological functions. In this perspective, we highlight the recent discovery of microproteins in the brain and describe several hypotheses that have emerged concerning microprotein function in the developing and mature nervous system.
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Affiliation(s)
- Erin E. Duffy
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Elena G. Assad
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Brian T. Kalish
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Division of Neonatology, Department of Paediatrics, Hospital for Sick Children, Toronto, ON, Canada
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Nichols C, Do-Thi VA, Peltier DC. Noncanonical microprotein regulation of immunity. Mol Ther 2024:S1525-0016(24)00324-1. [PMID: 38734902 DOI: 10.1016/j.ymthe.2024.05.021] [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: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.
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Affiliation(s)
- Cydney Nichols
- Morris Green Scholars Program, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Van Anh Do-Thi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daniel C Peltier
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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13
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Das D, Podder S. Microscale marvels: unveiling the macroscopic significance of micropeptides in human health. Brief Funct Genomics 2024:elae018. [PMID: 38706311 DOI: 10.1093/bfgp/elae018] [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: 01/04/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Non-coding RNA encodes micropeptides from small open reading frames located within the RNA. Interestingly, these micropeptides are involved in a variety of functions within the body. They are emerging as the resolving piece of the puzzle for complex biomolecular signaling pathways within the body. Recent studies highlight the pivotal role of small peptides in regulating important biological processes like DNA repair, gene expression, muscle regeneration, immune responses, etc. On the contrary, altered expression of micropeptides also plays a pivotal role in the progression of various diseases like cardiovascular diseases, neurological disorders and several types of cancer, including colorectal cancer, hepatocellular cancer, lung cancer, etc. This review delves into the dual impact of micropeptides on health and pathology, exploring their pivotal role in preserving normal physiological homeostasis and probing their involvement in the triggering and progression of diseases.
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Affiliation(s)
- Deepyaman Das
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
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14
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Singh AK. Rules and impacts of nonsense-mediated mRNA decay in the degradation of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1853. [PMID: 38741356 DOI: 10.1002/wrna.1853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality-control process that selectively degrades mRNAs having premature termination codon, upstream open reading frame, or unusually long 3'UTR. NMD detects such mRNAs and rapidly degrades them during initial rounds of translation in the eukaryotic cells. Since NMD is a translation-dependent cytoplasmic mRNA surveillance process, the noncoding RNAs were initially believed to be NMD-resistant. The sequence feature-based analysis has revealed that many putative long noncoding RNAs (lncRNAs) have short open reading frames, most of which have translation potential. Subsequent transcriptome-based molecular studies showed an association of a large set of such putative lncRNAs with translating ribosomes, and some of them produce stable and functionally active micropeptides. The translationally active lncRNAs typically have relatively longer and unprotected 3'UTR, which can induce their NMD-dependent degradation. This review defines the mechanism and regulation of NMD-dependent degradation of lncRNAs and its impact on biological processes related to the functions of lncRNAs or their encoded micropeptides. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anand Kumar Singh
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
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15
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Ma Y, Li J, Liu Y, Zhao H, Qi X, Sun Y, Chen J, Zhou J, Ma X, Wang L. Identification and exploration of a new M2 macrophage marker MTLN in alveolar echinococcosis. Int Immunopharmacol 2024; 131:111808. [PMID: 38457984 DOI: 10.1016/j.intimp.2024.111808] [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: 02/14/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
The pathogen of alveolar echinococcosis (AE) is Echinococcus multilocularis (E. multilocularis), which has the characteristics of diffuse infiltration and growth and has a high mortality rate. At present, the role of macrophages in AE infection has attracted more and more attention, but the new biomarkers and polarization mechanisms of macrophages are rarely studied. In this study, CIBERSORT and WGCNA algorithms were used to establish a weighted gene co-expression network, and MTLN was identified as a biological marker of M2-type macrophages, which participated in energy metabolism of macrophages and mediated inflammatory response, but the role of MTLN in AE was not studied. In this study, liver tissue samples from AE patients were collected and immunofluorescence co-localization showed the relationship between MTLN and macrophage distribution. E. multilocularis infected mouse model was established to analyze the expression of MTLN, liver fibrosis, and inflammatory reaction after E. multilocularis infection. The cell experiment simulated the liver microenvironment of E. multilocularis infected human body and analyzed the expression of MTLN by QRT-PCR and western blot in vitro. The data showed that liver fibrosis occurred in AE patients, and MTLN was activated near the focus. After E. multilocularis infected mice, the expression of MTLN increased with time. In the cell experiment, after the antigen of E. multilocularis protoscolex stimulated normal liver cells, the expression of MTLN increased 48 h, at this time, M2 was up-regulated and M1 was down-regulated. Therefore, MTLN may be the key gene to regulate the polarization of M2 macrophages and cause fibrosis.
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Affiliation(s)
- Yuyu Ma
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang 830011, China
| | - Jiajun Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang 830011, China
| | - Yumei Liu
- Xinjiang Medical University Affiliated Traditional Chinese Medicine Hospital, Xinjiang, China
| | - Hui Zhao
- The First Affiliated Hospital of Xinjiang Medical University, Medical Testing Center, Xinjiang, China
| | - Xinwei Qi
- The First Affiliated Hospital of Xinjiang Medical University, Medical Testing Center, Xinjiang, China
| | - Yuqin Sun
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang 830011, China
| | - Jiahui Chen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang 830011, China
| | - Jinping Zhou
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang 830011, China
| | - Xiumin Ma
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang 830011, China.
| | - Liang Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang 830011, China; The Fifth Affiliated Hospital of Xinjiang Medical University, Medical Testing Center, Xinjiang, China.
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16
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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.
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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
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17
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Tang S, Zhang J, Lou F, Zhou H, Cai X, Wang Z, Sun L, Sun Y, Li X, Fan L, Li Y, Jin X, Deng S, Yin Q, Bai J, Wang H, Wang H. A lncRNA Dleu2-encoded peptide relieves autoimmunity by facilitating Smad3-mediated Treg induction. EMBO Rep 2024; 25:1208-1232. [PMID: 38291338 PMCID: PMC10933344 DOI: 10.1038/s44319-024-00070-4] [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: 05/15/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
Micropeptides encoded by short open reading frames (sORFs) within long noncoding RNAs (lncRNAs) are beginning to be discovered and characterized as regulators of biological and pathological processes. Here, we find that lncRNA Dleu2 encodes a 17-amino-acid micropeptide, which we name Dleu2-17aa, that is abundantly expressed in T cells. Dleu2-17aa promotes inducible regulatory T (iTreg) cell generation by interacting with SMAD Family Member 3 (Smad3) and enhancing its binding to the Foxp3 conserved non-coding DNA sequence 1 (CNS1) region. Importantly, the genetic deletion of Dleu2-17aa in mice by start codon mutation impairs iTreg generation and worsens experimental autoimmune encephalomyelitis (EAE). Conversely, the exogenous supplementation of Dleu2-17aa relieves EAE. Our findings demonstrate an indispensable role of Dleu2-17aa in maintaining immune homeostasis and suggest therapeutic applications for this peptide in treating autoimmune diseases.
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Affiliation(s)
- Sibei Tang
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Junxun Zhang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fangzhou Lou
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Hong Zhou
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Xiaojie Cai
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Zhikai Wang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Libo Sun
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Yang Sun
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Xiangxiao Li
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Li Fan
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Yan Li
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Xinping Jin
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Siyu Deng
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Qianqian Yin
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Bai
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Hong Wang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Honglin Wang
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China.
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18
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Atakan MM, Türkel İ, Özerkliğ B, Koşar ŞN, Taylor DF, Yan X, Bishop DJ. Small peptides: could they have a big role in metabolism and the response to exercise? J Physiol 2024; 602:545-568. [PMID: 38196325 DOI: 10.1113/jp283214] [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: 10/19/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024] Open
Abstract
Exercise is a powerful non-pharmacological intervention for the treatment and prevention of numerous chronic diseases. Contracting skeletal muscles provoke widespread perturbations in numerous cells, tissues and organs, which stimulate multiple integrated adaptations that ultimately contribute to the many health benefits associated with regular exercise. Despite much research, the molecular mechanisms driving such changes are not completely resolved. Technological advancements beginning in the early 1960s have opened new avenues to explore the mechanisms responsible for the many beneficial adaptations to exercise. This has led to increased research into the role of small peptides (<100 amino acids) and mitochondrially derived peptides in metabolism and disease, including those coded within small open reading frames (sORFs; coding sequences that encode small peptides). Recently, it has been hypothesized that sORF-encoded mitochondrially derived peptides and other small peptides play significant roles as exercise-sensitive peptides in exercise-induced physiological adaptation. In this review, we highlight the discovery of mitochondrially derived peptides and newly discovered small peptides involved in metabolism, with a specific emphasis on their functions in exercise-induced adaptations and the prevention of metabolic diseases. In light of the few studies available, we also present data on how both single exercise sessions and exercise training affect expression of sORF-encoded mitochondrially derived peptides. Finally, we outline numerous research questions that await investigation regarding the roles of mitochondrially derived peptides in metabolism and prevention of various diseases, in addition to their roles in exercise-induced physiological adaptations, for future studies.
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Affiliation(s)
- Muhammed M Atakan
- Division of Exercise Nutrition and Metabolism, Faculty of Sport Sciences, Hacettepe University, Ankara, Turkey
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
| | - İbrahim Türkel
- Department of Exercise and Sport Sciences, Faculty of Sport Sciences, Hacettepe University, Ankara, Turkey
| | - Berkay Özerkliğ
- Department of Exercise and Sport Sciences, Faculty of Sport Sciences, Hacettepe University, Ankara, Turkey
| | - Şükran N Koşar
- Division of Exercise Nutrition and Metabolism, Faculty of Sport Sciences, Hacettepe University, Ankara, Turkey
| | - Dale F Taylor
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
| | - Xu Yan
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
- Sarcopenia Research Program, Australia Institute for Musculoskeletal Sciences (AIMSS), Melbourne, Victoria, Australia
| | - David J Bishop
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Victoria, Australia
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19
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Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. Mol Cell 2024; 84:261-276.e18. [PMID: 38176414 PMCID: PMC10872554 DOI: 10.1016/j.molcel.2023.12.003] [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: 05/16/2023] [Revised: 08/30/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.
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Affiliation(s)
- Damon A Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra L Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Sem A G Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin N Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA; Department of Pathology, Boston Children's Hospital, Boston MA 02115, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R Golub
- 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
| | - Pratiti Bandopadhayay
- 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
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.
| | - John R Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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20
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Baker ZN, Forny P, Pagliarini DJ. Mitochondrial proteome research: the road ahead. Nat Rev Mol Cell Biol 2024; 25:65-82. [PMID: 37773518 DOI: 10.1038/s41580-023-00650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 10/01/2023]
Abstract
Mitochondria are multifaceted organelles with key roles in anabolic and catabolic metabolism, bioenergetics, cellular signalling and nutrient sensing, and programmed cell death processes. Their diverse functions are enabled by a sophisticated set of protein components encoded by the nuclear and mitochondrial genomes. The extent and complexity of the mitochondrial proteome remained unclear for decades. This began to change 20 years ago when, driven by the emergence of mass spectrometry-based proteomics, the first draft mitochondrial proteomes were established. In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. The creation of these compendia provided a systemic view of an organelle previously studied primarily in a reductionist fashion and has accelerated both basic scientific discovery and the diagnosis and treatment of human disease. Yet numerous challenges remain in understanding mitochondrial biology and translating this knowledge into the medical context. In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. We highlight the power of an enhanced map for systematically defining the functions of its members. Finally, we examine the utility of an expanded, functionally annotated mitochondrial proteome in a translational setting for aiding both diagnosis of mitochondrial disease and targeting of mitochondria for treatment.
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Affiliation(s)
- Zakery N Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Forny
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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21
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Lu Y, Ran Y, Li H, Wen J, Cui X, Zhang X, Guan X, Cheng M. Micropeptides: origins, identification, and potential role in metabolism-related diseases. J Zhejiang Univ Sci B 2023; 24:1106-1122. [PMID: 38057268 PMCID: PMC10710913 DOI: 10.1631/jzus.b2300128] [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: 02/24/2023] [Accepted: 06/06/2023] [Indexed: 12/08/2023]
Abstract
With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides (miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function. MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.
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Affiliation(s)
| | | | | | | | | | | | | | - Min Cheng
- School of Basic Medicine Sciences, Weifang Medical University, Weifang 261053, China.
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22
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Ao YQ, Gao J, Jiang JH, Wang HK, Wang S, Ding JY. Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village. Mol Ther 2023; 31:3389-3413. [PMID: 37740493 PMCID: PMC10727995 DOI: 10.1016/j.ymthe.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.
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Affiliation(s)
- Yong-Qiang Ao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
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23
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Kore H, Datta KK, Nagaraj SH, Gowda H. Protein-coding potential of non-canonical open reading frames in human transcriptome. Biochem Biophys Res Commun 2023; 684:149040. [PMID: 37897910 DOI: 10.1016/j.bbrc.2023.09.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/09/2023] [Accepted: 09/23/2023] [Indexed: 10/30/2023]
Abstract
In recent years, proteogenomics and ribosome profiling studies have identified a large number of proteins encoded by noncoding regions in the human genome. They are encoded by small open reading frames (sORFs) in the untranslated regions (UTRs) of mRNAs and long non-coding RNAs (lncRNAs). These sORF encoded proteins (SEPs) are often <150AA and show poor evolutionary conservation. A subset of them have been functionally characterized and shown to play an important role in fundamental biological processes including cardiac and muscle function, DNA repair, embryonic development and various human diseases. How many novel protein-coding regions exist in the human genome and what fraction of them are functionally important remains a mystery. In this review, we discuss current progress in unraveling SEPs, approaches used for their identification, their limitations and reliability of these identifications. We also discuss functionally characterized SEPs and their involvement in various biological processes and diseases. Lastly, we provide insights into their distinctive features compared to canonical proteins and challenges associated with annotating these in protein reference databases.
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Affiliation(s)
- Hitesh Kore
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, 4059, Australia; Cancer Precision Medicine Group, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, 4006, Australia; Faculty of Health, Queensland University of Technology, Brisbane, Queensland, 4059, Australia.
| | - Keshava K Datta
- Proteomics and Metabolomics Platform, La Trobe University, Melbourne, VIC, 3083, Australia
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, 4059, Australia; Faculty of Health, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
| | - Harsha Gowda
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, 4059, Australia; Cancer Precision Medicine Group, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, 4006, Australia; Faculty of Health, Queensland University of Technology, Brisbane, Queensland, 4059, Australia; Faculty of Medicine, The University of Queensland, Queensland, 4072, Australia.
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24
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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.
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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.
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25
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Wang J, Wang W, Ma F, Qian H. A hidden translatome in tumors-the coding lncRNAs. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2755-2772. [PMID: 37154857 DOI: 10.1007/s11427-022-2289-6] [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: 11/08/2022] [Accepted: 12/29/2022] [Indexed: 05/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been extensively identified in eukaryotic genomes and have been shown to play critical roles in the development of multiple cancers. Through the application and development of ribosome analysis and sequencing technologies, advanced studies have discovered the translation of lncRNAs. Although lncRNAs were originally defined as noncoding RNAs, many lncRNAs actually contain small open reading frames that are translated into peptides. This opens a broad area for the functional investigation of lncRNAs. Here, we introduce prospective methods and databases for screening lncRNAs with functional polypeptides. We also summarize the specific lncRNA-encoded proteins and their molecular mechanisms that promote or inhibit cancerous. Importantly, the role of lncRNA-encoded peptides/proteins holds promise in cancer research, but some potential challenges remain unresolved. This review includes reports on lncRNA-encoded peptides or proteins in cancer, aiming to provide theoretical basis and related references to facilitate the discovery of more functional peptides encoded by lncRNA, and to further develop new anti-cancer therapeutic targets as well as clinical biomarkers of diagnosis and prognosis.
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Affiliation(s)
- Jinsong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wenna Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fei Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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26
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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: 5] [Impact Index Per Article: 5.0] [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.
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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
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27
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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.
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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.
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28
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Ahmadpour ST, Orre C, Bertevello PS, Mirebeau-Prunier D, Dumas JF, Desquiret-Dumas V. Breast Cancer Chemoresistance: Insights into the Regulatory Role of lncRNA. Int J Mol Sci 2023; 24:15897. [PMID: 37958880 PMCID: PMC10650504 DOI: 10.3390/ijms242115897] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a subclass of noncoding RNAs composed of more than 200 nucleotides without the ability to encode functional proteins. Given their involvement in critical cellular processes such as gene expression regulation, transcription, and translation, lncRNAs play a significant role in organism homeostasis. Breast cancer (BC) is the second most common cancer worldwide and evidence has shown a relationship between aberrant lncRNA expression and BC development. One of the main obstacles in BC control is multidrug chemoresistance, which is associated with the deregulation of multiple mechanisms such as efflux transporter activity, mitochondrial metabolism reprogramming, and epigenetic regulation as well as apoptosis and autophagy. Studies have shown the involvement of a large number of lncRNAs in the regulation of such pathways. However, the underlying mechanism is not clearly elucidated. In this review, we present the principal mechanisms associated with BC chemoresistance that can be directly or indirectly regulated by lncRNA, highlighting the importance of lncRNA in controlling BC chemoresistance. Understanding these mechanisms in deep detail may interest the clinical outcome of BC patients and could be used as therapeutic targets to overcome BC therapy resistance.
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Affiliation(s)
- Seyedeh Tayebeh Ahmadpour
- Nutrition, Croissance et Cancer, Inserm, UMR1069, Université de Tours, 37032 Tours, France; (P.S.B.); (J.-F.D.)
| | - Charlotte Orre
- Inserm U1083, UMR CNRS 6214, Angers University, 49933 Angers, France; (C.O.); (D.M.-P.)
| | - Priscila Silvana Bertevello
- Nutrition, Croissance et Cancer, Inserm, UMR1069, Université de Tours, 37032 Tours, France; (P.S.B.); (J.-F.D.)
| | | | - Jean-François Dumas
- Nutrition, Croissance et Cancer, Inserm, UMR1069, Université de Tours, 37032 Tours, France; (P.S.B.); (J.-F.D.)
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29
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Zhang L, Tang M, Diao H, Xiong L, Yang X, Xing S. LncRNA-encoded peptides: unveiling their significance in cardiovascular physiology and pathology-current research insights. Cardiovasc Res 2023; 119:2165-2178. [PMID: 37517040 DOI: 10.1093/cvr/cvad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/17/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), which are RNA transcripts exceeding 200 nucleotides were believed to lack any protein-coding capacity. But advancements in -omics technology have revealed that some lncRNAs have small open reading frames (sORFs) that can be translated by ribosomes to encode peptides, some of which have important biological functions. These encoded peptides subserve important biological functions by interacting with their targets to modulate transcriptional or signalling axes, thereby enhancing or suppressing cardiovascular disease (CVD) occurrence and progression. In this review, we summarize what is known about the research strategy of lncRNA-encoded peptides, mainly comprising predictive websites/tools and experimental methods that have been widely used for prediction, identification, and validation. More importantly, we have compiled a list of lncRNA- encoded peptides, with a focus on those that play significant roles in cardiovascular physiology and pathology, including ENSRNOT (RNO)-sORF6/RNO-sORF7/RNO-sORF8, dwarf open reading frame (DOWRF), myoregulin (NLN), etc. Additionally, we have outlined the functions and mechanisms of these peptides in cardiovascular physiology and pathology, such as cardiomyocyte hypertrophy, myocardial contraction, myocardial infarction, and vascular remodelling. Finally, an overview of the existing challenges and potential future developments in the realm of lncRNA-encoded peptides was provided, with consideration given to prospective avenues for further research. Given that many lncRNA-encoded peptides have not been functionally annotated yet, their application in CVD diagnosis and treatment still requires further research.
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Affiliation(s)
- Li Zhang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Mi Tang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Haoyang Diao
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Liling Xiong
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Xiao Yang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Shasha Xing
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
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30
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Kamradt ML, Makarewich CA. Mitochondrial microproteins: critical regulators of protein import, energy production, stress response pathways, and programmed cell death. Am J Physiol Cell Physiol 2023; 325:C807-C816. [PMID: 37642234 DOI: 10.1152/ajpcell.00189.2023] [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: 05/05/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
Mitochondria rely upon the coordination of protein import, protein translation, and proper functioning of oxidative phosphorylation (OXPHOS) complexes I-V to sustain the activities of life for an organism. Each process is dependent upon the function of profoundly large protein complexes found in the mitochondria [translocase of the outer mitochondrial membrane (TOMM) complex, translocase of the inner mitochondrial membrane (TIMM) complex, OXPHOS complexes, mitoribosomes]. These massive protein complexes, in some instances more than one megadalton, are built up from numerous protein subunits of varying sizes, including many proteins that are ≤100-150 amino acids. However, these small proteins, termed microproteins, not only act as cogs in large molecular machines but also have important steps in inhibiting or promoting the intrinsic pathway of apoptosis, coordinate responses to cellular stress, and even act as hormones. This review focuses on microproteins that occupy the mitochondria and are critical for its function. Although the microprotein field is relatively new, researchers have long recognized the existence of these mitochondrial proteins as critical components of virtually all aspects of mitochondrial biology. Thus, recent studies estimating that hundreds of new microproteins of unknown function exist and are missing from current genome annotations suggests that the mitochondrial "microproteome" is a rich area for future biological investigation.
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Affiliation(s)
- Michael L Kamradt
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - Catherine A Makarewich
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
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31
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Jacobs HT, Szibor M, Rathkolb B, da Silva-Buttkus P, Aguilar-Pimentel JA, Amarie OV, Becker L, Calzada-Wack J, Dragano N, Garrett L, Gerlini R, Hölter SM, Klein-Rodewald T, Kraiger M, Leuchtenberger S, Marschall S, Östereicher MA, Pfannes K, Sanz-Moreno A, Seisenberger C, Spielmann N, Stoeger C, Wurst W, Fuchs H, Hrabě de Angelis M, Gailus-Durner V. AOX delays the onset of the lethal phenotype in a mouse model of Uqcrh (complex III) disease. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166760. [PMID: 37230398 DOI: 10.1016/j.bbadis.2023.166760] [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: 03/09/2023] [Revised: 04/24/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
The alternative oxidase, AOX, provides a by-pass of the cytochrome segment of the mitochondrial respiratory chain when the chain is unavailable. AOX is absent from mammals, but AOX from Ciona intestinalis is benign when expressed in mice. Although non-protonmotive, so does not contribute directly to ATP production, it has been shown to modify and in some cases rescue phenotypes of respiratory-chain disease models. Here we studied the effect of C. intestinalis AOX on mice engineered to express a disease-equivalent mutant of Uqcrh, encoding the hinge subunit of mitochondrial respiratory complex III, which results in a complex metabolic phenotype beginning at 4-5 weeks, rapidly progressing to lethality within a further 6-7 weeks. AOX expression delayed the onset of this phenotype by several weeks, but provided no long-term benefit. We discuss the significance of this finding in light of the known and hypothesized effects of AOX on metabolism, redox homeostasis, oxidative stress and cell signaling. Although not a panacea, the ability of AOX to mitigate disease onset and progression means it could be useful in treatment.
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Affiliation(s)
- Howard T Jacobs
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Marten Szibor
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland; Department of Cardiothoracic Surgery, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Friedrich Schiller University of Jena, Am Klinikum 1, 07747 Jena, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University München, Feodor-Lynen Str. 25, 81377 Munich, Germany; German Center for Diabetes Research (DZD), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Patricia da Silva-Buttkus
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Juan Antonio Aguilar-Pimentel
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Nathalia Dragano
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Lillian Garrett
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Sabine M Hölter
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Tanja Klein-Rodewald
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Markus Kraiger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Stefanie Leuchtenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Susan Marschall
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Manuela A Östereicher
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Kristina Pfannes
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Adrián Sanz-Moreno
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Claudia Seisenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Claudia Stoeger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Chair of Developmental Genetics, TUM School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany; Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Feodor-Lynen-Str. 17, 81377 Munich, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany.
| | - Valérie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
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Zhang S, Guo Y, Fidelito G, Robinson DR, Liang C, Lim R, Bichler Z, Guo R, Wu G, Xu H, Zhou QD, Singh BK, Yen P, Kappei D, Stroud DA, Ho L. LINC00116-encoded microprotein mitoregulin regulates fatty acid metabolism at the mitochondrial outer membrane. iScience 2023; 26:107558. [PMID: 37664623 PMCID: PMC10469944 DOI: 10.1016/j.isci.2023.107558] [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: 12/05/2022] [Revised: 07/04/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
LINC00116 encodes a microprotein first identified as Mitoregulin (MTLN), where it was reported to localize to the inner membrane of mitochondria to regulate fatty acid oxidation and oxidative phosphorylation. These initial discoveries were followed by reports with differing findings about its molecular functions and submitochondrial localization. To clarify the apparent discrepancies, we constructed multiple orthogonal methods of determining the localization of MTLN, including split GFP-based reporters that enable efficient and reliable topology analyses for microproteins. These methods unequivocally demonstrate MTLN primarily localizes to the outer membrane of mitochondria, where it interacts with enzymes of fatty acid metabolism including CPT1B and CYB5B. Loss of MTLN causes the accumulation of very long-chain fatty acids (VLCFAs), especially docosahexaenoic acid (DHA). Intriguingly, loss of MTLN protects mice against western diet/fructose-induced insulin-resistance, suggests a protective effect of VLCFAs in this context. MTLN thus serves as an attractive target to control the catabolism of VLCFAs.
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Affiliation(s)
- Shan Zhang
- Department of Biochemistry, Department of Cardiology of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yabo Guo
- Department of Biochemistry, Department of Cardiology of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Gio Fidelito
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - David R.L. Robinson
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Chao Liang
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Radiance Lim
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Zoë Bichler
- Behavioral Neuroscience Laboratory, National Neuroscience Institute, Singapore 308433, Singapore
| | - Ruiyang Guo
- Department of Biochemistry, Department of Cardiology of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Gaoqi Wu
- Institute of Immunology, Department of Surgical Oncology of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - He Xu
- Institute of Immunology, Department of Surgical Oncology of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Quan D. Zhou
- Institute of Immunology, Department of Surgical Oncology of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Brijesh K. Singh
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Paul Yen
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Dennis Kappei
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - David A. Stroud
- Department of Biochemistry and Pharmacology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3010, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC 3010, Australia
| | - Lena Ho
- Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
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33
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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: 1.0] [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.
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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
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34
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Hassel KR, Brito-Estrada O, Makarewich CA. Microproteins: Overlooked regulators of physiology and disease. iScience 2023; 26:106781. [PMID: 37213226 PMCID: PMC10199267 DOI: 10.1016/j.isci.2023.106781] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Ongoing efforts to generate a complete and accurate annotation of the genome have revealed a significant blind spot for small proteins (<100 amino acids) originating from short open reading frames (sORFs). The recent discovery of numerous sORF-encoded proteins, termed microproteins, that play diverse roles in critical cellular processes has ignited the field of microprotein biology. Large-scale efforts are currently underway to identify sORF-encoded microproteins in diverse cell-types and tissues and specialized methods and tools have been developed to aid in their discovery, validation, and functional characterization. Microproteins that have been identified thus far play important roles in fundamental processes including ion transport, oxidative phosphorylation, and stress signaling. In this review, we discuss the optimized tools available for microprotein discovery and validation, summarize the biological functions of numerous microproteins, outline the promise for developing microproteins as therapeutic targets, and look forward to the future of the field of microprotein biology.
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Affiliation(s)
- Keira R. Hassel
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Omar Brito-Estrada
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Catherine A. Makarewich
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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35
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Kozuka-Hata H, Hiroki T, Miyamura N, Kitamura A, Tsumoto K, Inoue JI, Oyama M. Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames. Biomolecules 2023; 13:979. [PMID: 37371559 DOI: 10.3390/biom13060979] [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: 03/24/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Abnormal expression of histone deacetylases (HDACs) is reported to be associated with angiogenesis, metastasis and chemotherapy resistance regarding cancer in a wide range of previous studies. Suberoylanilide hydroxamic acid (SAHA) is well known to function as a pan-inhibitor for HDACs and recognized as one of the therapeutic drug candidates to epigenetically coordinate cancer cell fate regulation on a genomic scale. Here, we established a Real-Time Search (RTS)-assisted mass spectrometric platform for system-wide quantification of translated products encoded by non-canonical short open reading frames (ORFs) as well as already annotated protein coding sequences (CDSs) on the human transciptome and applied this methodology to quantitative proteomic analyses of suberoylanilide hydroxamic acid (SAHA)-treated human HeLa cells to evaluate proteome-wide regulation in response to drug perturbation. Very intriguingly, our RTS-based in-depth proteomic analysis enabled us to identify approximately 5000 novel peptides from the ribosome profiling-based short ORFs encoded in the diversified regions on presumed 'non-coding' nucleotide sequences of mRNAs as well as lncRNAs and nonsense mediated decay (NMD) transcripts. Furthermore, TMT-based multiplex large-scale quantification of the whole proteome changes upon differential SAHA treatment unveiled dose-dependent selective translational regulation of a limited fraction of the non-canonical short ORFs in addition to key cell cycle/proliferation-related molecules such as UBE2C, CENPF and PRC1. Our study provided the first system-wide landscape of drug-perturbed translational modulation on both canonical and non-canonical proteome dynamics in human cancer cells.
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Affiliation(s)
- Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Tomoko Hiroki
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Naoaki Miyamura
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Aya Kitamura
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jun-Ichiro Inoue
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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36
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Meng K, Lu S, Li Y, Hu L, Zhang J, Cao Y, Wang Y, Zhang CZ, He Q. LINC00493-encoded microprotein SMIM26 exerts anti-metastatic activity in renal cell carcinoma. EMBO Rep 2023; 24:e56282. [PMID: 37009826 PMCID: PMC10240204 DOI: 10.15252/embr.202256282] [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: 10/12/2022] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Human microproteins encoded by long non-coding RNAs (lncRNA) have been increasingly discovered, however, complete functional characterization of these emerging proteins is scattered. Here, we show that LINC00493-encoded SMIM26, an understudied microprotein localized in mitochondria, is tendentiously downregulated in clear cell renal cell carcinoma (ccRCC) and correlated with poor overall survival. LINC00493 is recognized by RNA-binding protein PABPC4 and transferred to ribosomes for translation of a 95-amino-acid protein SMIM26. SMIM26, but not LINC00493, suppresses ccRCC growth and metastatic lung colonization by interacting with acylglycerol kinase (AGK) and glutathione transport regulator SLC25A11 via its N-terminus. This interaction increases the mitochondrial localization of AGK and subsequently inhibits AGK-mediated AKT phosphorylation. Moreover, the formation of the SMIM26-AGK-SCL25A11 complex maintains mitochondrial glutathione import and respiratory efficiency, which is abrogated by AGK overexpression or SLC25A11 knockdown. This study functionally characterizes the LINC00493-encoded microprotein SMIM26 and establishes its anti-metastatic role in ccRCC, and therefore illuminates the importance of hidden proteins in human cancers.
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Affiliation(s)
- Kun Meng
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
- The First Affiliated Hospital of Jinan University and MOE Key Laboratory of Tumor Molecular Biology, Jinan UniversityGuangzhouChina
| | - Shaohua Lu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
- Sino‐French Hoffmann Institute, School of Basic Medical Sciences, State Key Laboratory of Respiratory DiseaseGuangzhou Medical UniversityGuangzhouChina
| | - Yu‐Ying Li
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
| | - Li‐Ling Hu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
| | - Jing Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
- The First Affiliated Hospital of Jinan University and MOE Key Laboratory of Tumor Molecular Biology, Jinan UniversityGuangzhouChina
| | - Yun Cao
- Department of Pathology, State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Yang Wang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
| | - Chris Zhiyi Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
| | - Qing‐Yu He
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan UniversityGuangzhouChina
- The First Affiliated Hospital of Jinan University and MOE Key Laboratory of Tumor Molecular Biology, Jinan UniversityGuangzhouChina
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37
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Talross GJS, Carlson JR. The rich non-coding RNA landscape of the Drosophila antenna. Cell Rep 2023; 42:112482. [PMID: 37167060 PMCID: PMC10431215 DOI: 10.1016/j.celrep.2023.112482] [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: 01/09/2023] [Revised: 03/07/2023] [Accepted: 04/20/2023] [Indexed: 05/13/2023] Open
Abstract
Emerging evidence suggests that long non-coding RNAs (lncRNAs) play diverse and critical roles in neural development, function, and disease. Here, we examine neuronal lncRNAs in a model system that offers enormous advantages for deciphering their functions: the Drosophila olfactory system. This system is numerically simple, its neurons are exquisitely well defined, and it drives multiple complex behaviors. We undertake a comprehensive survey of linear and circular lncRNAs in the Drosophila antenna and identify a wealth of lncRNAs enriched in it. We generate an unprecedented lncRNA-to-neuron map, which reveals that olfactory receptor neurons are defined not only by their receptors but also by the combination of lncRNAs they express. We identify species-specific lncRNAs, including many that are expressed primarily in pheromone-sensing neurons and that may act in modulation of pheromonal responses or in speciation. This resource opens many new opportunities for investigating the roles of lncRNAs in the nervous system.
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Affiliation(s)
- Gaëlle J S Talross
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - John R Carlson
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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38
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Averina OA, Permyakov OA, Emelianova MA, Guseva EA, Grigoryeva OO, Lovat ML, Egorova AE, Grinchenko AV, Kumeiko VV, Marey MV, Manskikh VN, Dontsova OA, Vyssokikh MY, Sergiev PV. Kidney-Related Function of Mitochondrial Protein Mitoregulin. Int J Mol Sci 2023; 24:ijms24109106. [PMID: 37240452 DOI: 10.3390/ijms24109106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
A small protein, Mitoregulin (Mtln), localizes in mitochondria and contributes to oxidative phosphorylation and fatty acid metabolism. Mtln knockout mice develop obesity on a high-fat diet, demonstrating elevated cardiolipin damage and suboptimal creatine kinase oligomerization in muscle tissue. Kidneys heavily depend on the oxidative phosphorylation in mitochondria. Here we report kidney-related phenotypes in aged Mtln knockout mice. Similar to Mtln knockout mice muscle mitochondria, those of the kidney demonstrate a decreased respiratory complex I activity and excessive cardiolipin damage. Aged male mice carrying Mtln knockout demonstrated an increased frequency of renal proximal tubules' degeneration. At the same time, a decreased glomerular filtration rate has been more frequently detected in aged female mice devoid of Mtln. An amount of Mtln partner protein, Cyb5r3, is drastically decreased in the kidneys of Mtln knockout mice.
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Affiliation(s)
- Olga A Averina
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Oleg A Permyakov
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Mariia A Emelianova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
| | - Ekaterina A Guseva
- Center for Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
| | - Olga O Grigoryeva
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Maxim L Lovat
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Institute of Mitoengineering MSU, 119992 Moscow, Russia
| | - Anna E Egorova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia
| | - Andrei V Grinchenko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, 690041 Vladivostok, Russia
| | - Vadim V Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia
- A.V. Zhirmunsky National Scientific Center of Marine Biology, 690041 Vladivostok, Russia
| | - Maria V Marey
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I.Kulakov, 117198 Moscow, Russia
| | - Vasily N Manskikh
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Institute of Mitoengineering MSU, 119992 Moscow, Russia
| | - Olga A Dontsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119992 Moscow, Russia
| | - Mikhail Y Vyssokikh
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I.Kulakov, 117198 Moscow, Russia
| | - Petr V Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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39
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Romerio F. Origin and functional role of antisense transcription in endogenous and exogenous retroviruses. Retrovirology 2023; 20:6. [PMID: 37194028 DOI: 10.1186/s12977-023-00622-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/30/2023] [Indexed: 05/18/2023] Open
Abstract
Most proteins expressed by endogenous and exogenous retroviruses are encoded in the sense (positive) strand of the genome and are under the control of regulatory elements within the 5' long terminal repeat (LTR). A number of retroviral genomes also encode genes in the antisense (negative) strand and their expression is under the control of negative sense promoters within the 3' LTR. In the case of the Human T-cell Lymphotropic Virus 1 (HTLV-1), the antisense protein HBZ has been shown to play a critical role in the virus lifecycle and in the pathogenic process, while the function of the Human Immunodeficiency Virus 1 (HIV-1) antisense protein ASP remains unknown. However, the expression of 3' LTR-driven antisense transcripts is not always demonstrably associated with the presence of an antisense open reading frame encoding a viral protein. Moreover, even in the case of retroviruses that do express an antisense protein, such as HTLV-1 and the pandemic strains of HIV-1, the 3' LTR-driven antisense transcript shows both protein-coding and noncoding activities. Indeed, the ability to express antisense transcripts appears to be phylogenetically more widespread among endogenous and exogenous retroviruses than the presence of a functional antisense open reading frame within these transcripts. This suggests that retroviral antisense transcripts may have originated as noncoding molecules with regulatory activity that in some cases later acquired protein-coding function. Here, we will review examples of endogenous and exogenous retroviral antisense transcripts, and the ways through which they benefit viral persistence in the host.
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Affiliation(s)
- Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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40
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Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SA, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539399. [PMID: 37205492 PMCID: PMC10187264 DOI: 10.1101/2023.05.04.539399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames. To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a step-wise approach to employ multiple CRISPR-Cas9 screens to elucidate functional non-canonical ORFs implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream open reading frames (uORFs) exhibited selective functionality independent of the main coding sequence. One of these, ASNSD1-uORF or ASDURF, was upregulated, associated with the MYC family oncogenes, and was required for medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future cancer genomics studies seeking to define new cancer targets.
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Affiliation(s)
- Damon A. Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
- These authors contributed equally
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- These authors contributed equally
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Current address: Arbor Biotechnologies, Cambridge, MA, 02140, USA
| | - Karl R. Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alexandra L. Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T. van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Sem A.G. Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin N. Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Current address: Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02215, USA
| | - Keith L. Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02215, USA
- Department of Pathology, Boston Children’s Hospital, Boston MA 02115
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45229, USA
| | | | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Charité-Universitätsmedizin, 10117 Berlin, Germany
- German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R. Golub
- 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
| | - Pratiti Bandopadhayay
- 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
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - 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
- Current address: Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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41
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Jain N, Richter F, Adzhubei I, Sharp AJ, Gelb BD. Small open reading frames: a comparative genetics approach to validation. BMC Genomics 2023; 24:226. [PMID: 37127568 PMCID: PMC10152738 DOI: 10.1186/s12864-023-09311-7] [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: 07/14/2022] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the human genome, but the true number and the biological significance of the micropeptides they encode remain uncertain. Here, we used a comparative genomics approach to identify high-confidence smORFs that are likely protein-coding. We identified 3,326 high-confidence smORFs using constraint within human populations and evolutionary conservation as additional lines of evidence. Next, we validated that, as a group, our high-confidence smORFs are conserved at the amino-acid level rather than merely residing in highly conserved non-coding regions. Finally, we found that high-confidence smORFs are enriched among disease-associated variants from GWAS. Overall, our results highlight that smORF-encoded peptides likely have important functional roles in human disease.
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Affiliation(s)
- Niyati Jain
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, New York, NY, 10029, USA
- Present Address: Committee On Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Felix Richter
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ivan Adzhubei
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, 1470 Madison Avenue, New York, NY, 10029, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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42
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Seal RL, Tweedie S, Bruford EA. A standardised nomenclature for long non-coding RNAs. IUBMB Life 2023; 75:380-389. [PMID: 35880706 PMCID: PMC9877250 DOI: 10.1002/iub.2663] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/08/2022] [Indexed: 01/29/2023]
Abstract
The HUGO Gene Nomenclature Committee (HGNC) is the sole group with the authority to approve symbols for human genes, including long non-coding RNA (lncRNA) genes. Use of approved symbols ensures that publications and biomedical databases are easily searchable and reduces the risks of confusion that can be caused by using the same symbol to refer to different genes or using many different symbols for the same gene. Here, we describe how the HGNC names lncRNA genes and review the nomenclature of the seven lncRNA genes most mentioned in the scientific literature.
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Affiliation(s)
- Ruth L. Seal
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
- Department of HaematologyUniversity of Cambridge School of Clinical MedicineCambridgeUK
| | - Susan Tweedie
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
| | - Elspeth A. Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome CampusHinxtonUK
- Department of HaematologyUniversity of Cambridge School of Clinical MedicineCambridgeUK
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43
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Averina OA, Permyakov OA, Emelianova MA, Grigoryeva OO, Lovat ML, Egorova AE, Grinchenko AV, Kumeiko VV, Marey MV, Manskikh VN, Dontsova OA, Vysokikh MY, Sergiev PV. Mitoregulin Contributes to Creatine Shuttling and Cardiolipin Protection in Mice Muscle. Int J Mol Sci 2023; 24:ijms24087589. [PMID: 37108753 PMCID: PMC10143810 DOI: 10.3390/ijms24087589] [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: 03/03/2023] [Revised: 04/06/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Small peptides compose a large share of the mitochondrial proteome. Mitoregulin (Mtln) is a mitochondrial peptide known to contribute to the respiratory complex I functioning and other processes in mitochondria. In our previous studies, we demonstrated that Mtln knockout mice develop obesity and accumulate triglycerides and other oxidation substrates in serum, concomitant with an exhaustion of tricarboxylic acids cycle intermediates. Here we examined the functional role of Mtln in skeletal muscles, one of the major energy consuming tissues. We observed reduced muscle strength for Mtln knockout mice. Decrease of the mitochondrial cardiolipin and concomitant increase in monolysocardiolipin concentration upon Mtln inactivation is likely to be a consequence of imbalance between oxidative damage and remodeling of cardiolipin. It is accompanied by the mitochondrial creatine kinase octamer dissociation and suboptimal respiratory chain performance in Mtln knockout mice.
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Affiliation(s)
- Olga A Averina
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Oleg A Permyakov
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Mariia A Emelianova
- Center for Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
| | - Olga O Grigoryeva
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Maxim L Lovat
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Institute of Mitoengineering MSU, 119992 Moscow, Russia
| | - Anna E Egorova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia
| | - Andrei V Grinchenko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, 690041 Vladivostok, Russia
| | - Vadim V Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia
- A.V. Zhirmunsky National Scientific Center of Marine Biology, 690041 Vladivostok, Russia
| | - Maria V Marey
- Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Vasily N Manskikh
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Institute of Mitoengineering MSU, 119992 Moscow, Russia
| | - Olga A Dontsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119992 Moscow, Russia
| | - Mikhail Yu Vysokikh
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Research Center for Obstetrics, Gynecology and Perinatology, 117198 Moscow, Russia
| | - Petr V Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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44
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Miller B, Kim SJ, Mehta HH, Cao K, Kumagai H, Thumaty N, Leelaprachakul N, Braniff RG, Jiao H, Vaughan J, Diedrich J, Saghatelian A, Arpawong TE, Crimmins EM, Ertekin-Taner N, Tubi MA, Hare ET, Braskie MN, Décarie-Spain L, Kanoski SE, Grodstein F, Bennett DA, Zhao L, Toga AW, Wan J, Yen K, Cohen P. Mitochondrial DNA variation in Alzheimer's disease reveals a unique microprotein called SHMOOSE. Mol Psychiatry 2023; 28:1813-1826. [PMID: 36127429 PMCID: PMC10027624 DOI: 10.1038/s41380-022-01769-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 08/15/2022] [Accepted: 08/26/2022] [Indexed: 01/22/2023]
Abstract
Mitochondrial DNA variants have previously associated with disease, but the underlying mechanisms have been largely elusive. Here, we report that mitochondrial SNP rs2853499 associated with Alzheimer's disease (AD), neuroimaging, and transcriptomics. We mapped rs2853499 to a novel mitochondrial small open reading frame called SHMOOSE with microprotein encoding potential. Indeed, we detected two unique SHMOOSE-derived peptide fragments in mitochondria by using mass spectrometry-the first unique mass spectrometry-based detection of a mitochondrial-encoded microprotein to date. Furthermore, cerebrospinal fluid (CSF) SHMOOSE levels in humans correlated with age, CSF tau, and brain white matter volume. We followed up on these genetic and biochemical findings by carrying out a series of functional experiments. SHMOOSE acted on the brain following intracerebroventricular administration, differentiated mitochondrial gene expression in multiple models, localized to mitochondria, bound the inner mitochondrial membrane protein mitofilin, and boosted mitochondrial oxygen consumption. Altogether, SHMOOSE has vast implications for the fields of neurobiology, Alzheimer's disease, and microproteins.
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Affiliation(s)
- Brendan Miller
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | - Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kevin Cao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hiroshi Kumagai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Neehar Thumaty
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Naphada Leelaprachakul
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Regina Gonzalez Braniff
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Henry Jiao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jolene Diedrich
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Thalida E Arpawong
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eileen M Crimmins
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | | | - Meral A Tubi
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Evan T Hare
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Meredith N Braskie
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Léa Décarie-Spain
- Human and Evolutionary Biology Section, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Scott E Kanoski
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
- Human and Evolutionary Biology Section, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Francine Grodstein
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Lu Zhao
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Junxiang Wan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kelvin Yen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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45
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Shiny transcriptional junk: lncRNA-derived peptides in cancers and immune responses. Life Sci 2023; 316:121434. [PMID: 36706831 DOI: 10.1016/j.lfs.2023.121434] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023]
Abstract
By interacting with DNA, RNA, and proteins, long noncoding RNAs (lncRNAs) have been linked to several pathological states. LncRNA-derived peptides, as a novel modality of action of lncRNAs, have recently become a research hotspot. An increasing body of evidence has demonstrated the important role of these peptides in carcinogenesis and cancer progression and immune response. This review first describes lncRNA-derived peptides, the regulators that control their translation, and the roles of these peptides in multiple biological processes and disease states including cancers. In the following section, we comprehensively analyzed the significant role lncRNA-derived peptide played in the immune response. This review provides fresh perspectives on the biological role of lncRNAs and their relationship with diseases, particularly with cancers and the immune response, providing a theoretical basis for these lncRNA-derived peptides as therapeutic and diagnostic targets in cancers and inflammatory diseases.
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46
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Clauwaert J, McVey Z, Gupta R, Menschaert G. TIS Transformer: remapping the human proteome using deep learning. NAR Genom Bioinform 2023; 5:lqad021. [PMID: 36879896 PMCID: PMC9985340 DOI: 10.1093/nargab/lqad021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/20/2023] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
The correct mapping of the proteome is an important step towards advancing our understanding of biological systems and cellular mechanisms. Methods that provide better mappings can fuel important processes such as drug discovery and disease understanding. Currently, true determination of translation initiation sites is primarily achieved by in vivo experiments. Here, we propose TIS Transformer, a deep learning model for the determination of translation start sites solely utilizing the information embedded in the transcript nucleotide sequence. The method is built upon deep learning techniques first designed for natural language processing. We prove this approach to be best suited for learning the semantics of translation, outperforming previous approaches by a large margin. We demonstrate that limitations in the model performance are primarily due to the presence of low-quality annotations against which the model is evaluated against. Advantages of the method are its ability to detect key features of the translation process and multiple coding sequences on a transcript. These include micropeptides encoded by short Open Reading Frames, either alongside a canonical coding sequence or within long non-coding RNAs. To demonstrate the use of our methods, we applied TIS Transformer to remap the full human proteome.
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Affiliation(s)
- Jim Clauwaert
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Oost-Vlaanderen 9000, Belgium
| | - Zahra McVey
- Novo Nordisk Research Centre Oxford, Novo Nordisk Ltd., Crawley, South East England, RH6 0PA, UK
| | - Ramneek Gupta
- Novo Nordisk Research Centre Oxford, Novo Nordisk Ltd., Crawley, South East England, RH6 0PA, UK
| | - Gerben Menschaert
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Oost-Vlaanderen 9000, Belgium
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47
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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: 4.0] [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.
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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.
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48
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A lncRNA-encoded mitochondrial micropeptide exacerbates microglia-mediated neuroinflammation in retinal ischemia/reperfusion injury. Cell Death Dis 2023; 14:126. [PMID: 36792584 PMCID: PMC9932084 DOI: 10.1038/s41419-023-05617-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/17/2023]
Abstract
As a common pathology of many ocular disorders such as diabetic retinopathy and glaucoma, retinal ischemia/reperfusion (IR) triggers inflammation and microglia activation that lead to irreversible retinal damage. The detailed molecular mechanism underlying retinal IR injury, however, remains poorly understood at present. Here we report the bioinformatic identification of a lncRNA 1810058I24Rik (181-Rik) that was shown to encode a mitochondrion-located micropeptide Stmp1. Its deficiency in mice protected retinal ganglion cells from retinal IR injury by attenuating the activation of microglia and the Nlrp3 inflammasome pathway. Moreover, its genetic knockout in mice or knockdown in primary microglia promoted mitochondrial fusion, impaired mitochondrial membrane potential, and reactive oxygen species (ROS) production, diminished aerobic glycolysis, and ameliorated inflammation. It appears that 181-Rik may trigger the Nlrp3 inflammasome activation by controlling mitochondrial functions through inhibiting expression of the metabolic sensor uncoupling protein 2 (Ucp2) and activating expression of the Ca2+ sensors S100a8/a9. Together, our findings shed new light on the molecular pathogenesis of retinal IR injury and may provide a fresh therapeutic target for IR-associated neurodegenerative diseases.
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49
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Cassidy L, Kaulich PT, Tholey A. Proteoforms expand the world of microproteins and short open reading frame-encoded peptides. iScience 2023; 26:106069. [PMID: 36818287 PMCID: PMC9929600 DOI: 10.1016/j.isci.2023.106069] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Microproteins and short open reading frame-encoded peptides (SEPs) can, like all proteins, carry numerous posttranslational modifications. Together with posttranscriptional processes, this leads to a high number of possible distinct protein molecules, the proteoforms, out of a limited number of genes. The identification, quantification, and molecular characterization of proteoforms possess special challenges to established, mainly bottom-up proteomics (BUP) based analytical approaches. While BUP methods are powerful, proteins have to be inferred rather than directly identified, which hampers the detection of proteoforms. An alternative approach is top-down proteomics (TDP) which allows to identify intact proteoforms. This perspective article provides a brief overview of modified microproteins and SEPs, introduces the proteoform terminology, and compares present BUP and TDP workflows highlighting their major advantages and caveats. Necessary future developments in TDP to fully accentuate its potential for proteoform-centric analytics of microproteins and SEPs will be discussed.
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Affiliation(s)
- Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Philipp T. Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany,Corresponding author
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Zhang L, Di L, Liu J, Lei X, Gu M, Zhang W, Wang Y. The LncRNA signature associated with cuproptosis as a novel biomarker of prognosis in immunotherapy and drug screening for clear cell renal cell carcinoma. Front Genet 2023; 14:1039813. [PMID: 36755568 PMCID: PMC9899836 DOI: 10.3389/fgene.2023.1039813] [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: 09/23/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Cuproptosis is a new form of cell death, the second form of metal ion-induced cell death defined after ferroptosis. Recently, cuproptosis has been suggested to be associated with tumorigenesis. However, the relationship between cuproptosis and patient prognosis in clear cell renal cell carcinoma (ccRCC) in the context of immunotherapy remains unknown. The aim of this study was to investigate the correlation between cuproptosis-related long non-coding RNA (lncRNA) and ccRCC in terms of immunity as well as prognosis. Clinical information on lncRNAs associated with differences in cuproptosis genes in ccRCC and normal tissues was collected from The Cancer Genome Atlas (TCGA) dataset. Univariate Cox regression was used to screen lncRNAs. A total of 11 lncRNAs closely associated with cuproptosis were further screened and established using the least absolute shrinkage and selection operator (LASSO) algorithm and multivariate Cox regression, and the samples were randomly divided into training and test groups. A risk prognostic model was constructed using the training group, and the model was validated using the test group. We investigated the predictive ability of the prognostic risk model in terms of clinical prognosis, tumor mutation, immune escape, immunotherapy, tumor microenvironment, immune infiltration levels, and tumor drug treatment of ccRCC. Using the median risk score, patients were divided into low and high-risk groups. Kaplan-Meier curves showed that the overall survival (OS) of patients in the high-risk group was significantly worse than low-risk group (p < 0.001). Receiver operating characteristic (ROC) curves further validated the reliability of our model. The model consistently and accurately predicted prognosis at 1, 3, and 5 years, with an AUC above 0.7. Tumor cell genes generally precede morphological abnormalities; therefore, the model we constructed can effectively compensate for the traditional method of evaluating the prognosis of patients with renal cancer, and our model was also clinically meaningful in predicting ccRCC staging. In addition, lower model risk scores determined by mutational load indicated a good chance of survival. The high-risk group had greater recruitment of immune cells, while the anti-immune checkpoint immunotherapy was less efficacious overall than that of the low-risk group. Tumor and immune-related pathways were enriched, and anti-tumor agents were selected to improve the survival of ccRCC. This prognostic risk model is based on the levels of cuproptosis-associated lncRNAs and provides a new perspective in the clinical assessment and precise treatment of ccRCC.
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Affiliation(s)
- Lishuo Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Longjiang Di
- College of Basic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jinhui Liu
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xianli Lei
- Harbin Medical University, Harbin, Heilongjiang, China
| | - Maoli Gu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wenjing Zhang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Yufu Wang, ; Wenjing Zhang,
| | - Yufu Wang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Yufu Wang, ; Wenjing Zhang,
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