1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
|
4
|
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.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Cui M, Bezprozvannaya S, Hao T, Elnwasany A, Szweda LI, Liu N, Bassel-Duby R, Olson EN. Transcription factor NFYa controls cardiomyocyte metabolism and proliferation during mouse fetal heart development. Dev Cell 2023; 58:2867-2880.e7. [PMID: 37972593 PMCID: PMC11000264 DOI: 10.1016/j.devcel.2023.10.012] [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: 05/31/2023] [Revised: 08/22/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Cardiomyocytes are highly metabolic cells responsible for generating the contractile force in the heart. During fetal development and regeneration, these cells actively divide but lose their proliferative activity in adulthood. The mechanisms that coordinate their metabolism and proliferation are not fully understood. Here, we study the role of the transcription factor NFYa in developing mouse hearts. Loss of NFYa alters cardiomyocyte composition, causing a decrease in immature regenerative cells and an increase in trabecular and mature cardiomyocytes, as identified by spatial and single-cell transcriptome analyses. NFYa-deleted cardiomyocytes exhibited reduced proliferation and impaired mitochondrial metabolism, leading to cardiac growth defects and embryonic death. NFYa, interacting with cofactor SP2, activates genes linking metabolism and proliferation at the transcription level. Our study identifies a nodal role of NFYa in regulating prenatal cardiac growth and a previously unrecognized transcriptional control mechanism of heart metabolism, highlighting the importance of mitochondrial metabolism during heart development and regeneration.
Collapse
Affiliation(s)
- Miao Cui
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Tian Hao
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA
| | - Abdallah Elnwasany
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Luke I Szweda
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
| |
Collapse
|
8
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Min Cheng
- School of Basic Medicine Sciences, Weifang Medical University, Weifang 261053, China.
| |
Collapse
|
9
|
Sahgal A, Uversky V, Davé V. Microproteins transitioning into a new Phase: Defining the undefined. Methods 2023; 220:38-54. [PMID: 37890707 DOI: 10.1016/j.ymeth.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Recent advancements in omics technologies have unveiled a hitherto unknown group of short polypeptides called microproteins (miPs). Despite their size, accumulating evidence has demonstrated that miPs exert varied and potent biological functions. They act in paracrine, juxtracrine, and endocrine fashion, maintaining cellular physiology and driving diseases. The present study focuses on biochemical and biophysical analysis and characterization of twenty-four human miPs using distinct computational methods, including RIDAO, AlphaFold2, D2P2, FuzDrop, STRING, and Emboss Pep wheel. miPs often lack well-defined tertiary structures and may harbor intrinsically disordered regions (IDRs) that play pivotal roles in cellular functions. Our analyses define the physicochemical properties of an essential subset of miPs, elucidating their structural characteristics and demonstrating their propensity for driving or participating in liquid-liquid phase separation (LLPS) and intracellular condensate formation. Notably, miPs such as NoBody and pTUNAR revealed a high propensity for LLPS, implicating their potential involvement in forming membrane-less organelles (MLOs) during intracellular LLPS and condensate formation. The results of our study indicate that miPs have functionally profound implications in cellular compartmentalization and signaling processes essential for regulating normal cellular functions. Taken together, our methodological approach explains and highlights the biological importance of these miPs, providing a deeper understanding of the unusual structural landscape and functionality of these newly defined small proteins. Understanding their functions and biological behavior will aid in developing targeted therapies for diseases that involve miPs.
Collapse
Affiliation(s)
- Aayushi Sahgal
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vrushank Davé
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Pathology and Cell Biology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States.
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alina A. Martel
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Li K, Li B, Zhang D, Du T, Zhou H, Dai G, Yan Y, Gao N, Zhuang X, Liao X, Liu C, Dong Y, Chen D, Qu LH, Ou J, Yang JH, Huang ZP. The translational landscape of human vascular smooth muscle cells identifies novel short open reading frame-encoded peptide regulators for phenotype alteration. Cardiovasc Res 2023; 119:1763-1779. [PMID: 36943764 DOI: 10.1093/cvr/cvad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 03/23/2023] Open
Abstract
AIMS The plasticity of vascular smooth muscle cells (VSMCs) enables them to alter phenotypes under various physiological and pathological stimuli. The alteration of VSMC phenotype is a key step in vascular diseases, including atherosclerosis. Although the transcriptome shift during VSMC phenotype alteration has been intensively investigated, uncovering multiple key regulatory signalling pathways, the translatome dynamics in this cellular process, remain largely unknown. Here, we explored the genome-wide regulation at the translational level of human VSMCs during phenotype alteration. METHODS AND RESULTS We generated nucleotide-resolution translatome and transcriptome data from human VSMCs undergoing phenotype alteration. Deep sequencing of ribosome-protected fragments (Ribo-seq) revealed alterations in protein synthesis independent of changes in messenger ribonucleicacid levels. Increased translational efficiency of many translational machinery components, including ribosomal proteins, eukaryotic translation elongation factors and initiation factors were observed during the phenotype alteration of VSMCs. In addition, hundreds of candidates for short open reading frame-encoded polypeptides (SEPs), a class of peptides containing 200 amino acids or less, were identified in a combined analysis of translatome and transcriptome data with a high positive rate in validating their coding capability. Three evolutionarily conserved SEPs were further detected endogenously by customized antibodies and suggested to participate in the pathogenesis of atherosclerosis by analysing the transcriptome and single cell RNA-seq data from patient atherosclerotic artery samples. Gain- and loss-of-function studies in human VSMCs and genetically engineered mice showed that these SEPs modulate the alteration of VSMC phenotype through different signalling pathways, including the mitogen-activated protein kinase pathway and p53 pathway. CONCLUSION Our study indicates that an increase in the capacity of translation, which is attributable to an increased quantity of translational machinery components, mainly controls alterations of VSMC phenotype at the level of translational regulation. In addition, SEPs could function as important regulators in the phenotype alteration of human VSMCs.
Collapse
Affiliation(s)
- Kang Li
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Bin Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, 135 Xingang Xi Road, Guangzhou 510275, China
| | - Dihua Zhang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Tailai Du
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Huimin Zhou
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Gang Dai
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Youchen Yan
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Nailin Gao
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Xiaodong Zhuang
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Xinxue Liao
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Chen Liu
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Yugang Dong
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Demeng Chen
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, 135 Xingang Xi Road, Guangzhou 510275, China
| | - Jingsong Ou
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, 135 Xingang Xi Road, Guangzhou 510275, China
| | - Zhan-Peng Huang
- 1Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Er Road, Guangzhou 510080, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases (Sun Yat-sen University), 58 Zhongshan Er Road, Guangzhou 510080, China
| |
Collapse
|
16
|
Chen Y, Cao X, Loh KH, Slavoff SA. Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides. Biochem Soc Trans 2023; 51:1071-1082. [PMID: 37171061 PMCID: PMC10317152 DOI: 10.1042/bst20221074] [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: 01/03/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023]
Abstract
Thousands of unannotated small and alternative open reading frames (smORFs and alt-ORFs, respectively) have recently been revealed in mammalian genomes. While hundreds of mammalian smORF- and alt-ORF-encoded proteins (SEPs and alt-proteins, respectively) affect cell proliferation, the overwhelming majority of smORFs and alt-ORFs remain uncharacterized at the molecular level. Complicating the task of identifying the biological roles of smORFs and alt-ORFs, the SEPs and alt-proteins that they encode exhibit limited sequence homology to protein domains of known function. Experimental techniques for the functionalization of these gene classes are therefore required. Approaches combining chemical labeling and quantitative proteomics have greatly advanced our ability to identify and characterize functional SEPs and alt-proteins in high throughput. In this review, we briefly describe the principles of proteomic discovery of SEPs and alt-proteins, then summarize how these technologies interface with chemical labeling for identification of SEPs and alt-proteins with specific properties, as well as in defining the interactome of SEPs and alt-proteins.
Collapse
Affiliation(s)
- Yanran Chen
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, U.S.A
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ken H. Loh
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, U.S.A
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, U.S.A
| |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Xiaoping Dong
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Kun Zhang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Chengfeng Xun
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Tianqi Chu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Songping Liang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| | - Yong Zeng
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zhonghua Liu
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
- Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, Hunan Normal University, Changsha 410081, China
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Cai J, Dong Z. Two-way communication between the nucleus and mitochondria via a micropeptide in renal fibrosis. Kidney Int 2023; 103:833-835. [PMID: 37085255 DOI: 10.1016/j.kint.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 04/23/2023]
Abstract
Micropeptides are small proteins encoded by short open reading frames mostly located in long noncoding RNAs. Mitoregulin (MOXI) is a nuclear encoded micropeptide initially identified in the inner mitochondrial membrane to regulate fatty acid β-oxidation. In this issue of Kidney International, Li et al. report that MOXI is upregulated in both human fibrotic kidneys and murine models of renal fibrosis. Remarkably, MOXI functions in the nucleus, where it forms a transcriptional complex with N-acetyltransferase 14 and c-Jun to facilitate the expression of fibrotic genes. By working in the nucleus and mitochondria, MOXI may channel the 2-way communication between these organelles, adding a new layer of complexity in the cell biology of renal fibrogenesis.
Collapse
Affiliation(s)
- Juan Cai
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
| | - Zheng Dong
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China; Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia, USA.
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Malloy CR, Sherry AD, Alger JR, Jin ES. Recent progress in analysis of intermediary metabolism by ex vivo 13 C NMR. NMR IN BIOMEDICINE 2023; 36:e4817. [PMID: 35997012 DOI: 10.1002/nbm.4817] [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: 06/10/2022] [Revised: 08/03/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Advanced imaging technologies, large-scale metabolomics, and the measurement of gene transcripts or enzyme expression all enable investigations of intermediary metabolism in human patients. Complementary information about fluxes in individual metabolic pathways may be obtained by ex vivo 13 C NMR of blood or tissue biopsies. Simple molecules such as 13 C-labeled glucose are readily administered to patients prior to surgical biopsies, and 13 C-labeled glycerol is easily administered orally to outpatients. Here, we review recent progress in practical applications of 13 C NMR to study cancer biology, the response to oxidative stress, gluconeogenesis, triglyceride synthesis in patients, as well as new insights into compartmentation of metabolism in the cytosol. The technical aspects of obtaining the sample, preparing material for analysis, and acquiring the spectra are relatively simple. This approach enables convenient, valuable, and quantitative insights into intermediary metabolism in patients.
Collapse
Affiliation(s)
- Craig R Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Veterans Affairs North Texas Healthcare System, Dallas, Texas, USA
| | - A Dean Sherry
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Chemistry, University of Texas at Dallas, Richardson, Texas, USA
| | - Jeffry R Alger
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Neurology, Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Eunsook S Jin
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
24
|
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.
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
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.
Collapse
Affiliation(s)
- Jinhua Li
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China; Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia; Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Xinli Qu
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Chengnong Guan
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Ning Luo
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Huiting Chen
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Andy Li
- Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia
| | - Hongjie Zhuang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiayi Yang
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Hui Diao
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Shuhan Zeng
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qing Wang
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Jinjin Fan
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Mengjie Jiang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Bai
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhiming Ye
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoyun Jiang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - David J Nikolic-Paterson
- Department of Nephrology, Monash Health and Monash University Department of Medicine, Clayton, Victoria, Australia
| | - Xueqing Yu
- Department of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China.
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Wan L, Xiao W, Huang Z, Zhou A, Jiang Y, Zou B, Liu B, Deng C, Zhang Y. Systematic identification of smORFs in domestic silkworm ( Bombyx mori). PeerJ 2023; 11:e14682. [PMID: 36655040 PMCID: PMC9841908 DOI: 10.7717/peerj.14682] [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: 10/12/2022] [Accepted: 12/13/2022] [Indexed: 01/15/2023] Open
Abstract
The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our results showed that at least 738 highly reliable smORFs were found in B. mori and that 34,401 possible smORFs were partially supported. We also identified some differentially expressed and tissue-specific-expressed smORFs, which may be closely related to the characteristics and functions of the tissues. This article provides a basis for subsequent research on smORFs in silkworm, and also hopes to provide a reference point for future research methods for smORFs in other species.
Collapse
Affiliation(s)
- Linrong Wan
- Sericultural Research Institute,Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China,College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wenfu Xiao
- Sericultural Research Institute,Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Ziyan Huang
- Research and Development Center, LyuKang, Chengdu, Sichuan, China,Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, Sichuan, China
| | - Anlian Zhou
- Sericultural Research Institute,Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Yaming Jiang
- Sericultural Research Institute,Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Bangxing Zou
- Sericultural Research Institute,Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Binbin Liu
- Sericultural Research Institute,Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Cao Deng
- Research and Development Center, LyuKang, Chengdu, Sichuan, China,Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, Sichuan, China
| | - Youhong Zhang
- Sericultural Research Institute,Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| |
Collapse
|
29
|
Martinez TF, Lyons-Abbott S, Bookout AL, De Souza EV, Donaldson C, Vaughan JM, Lau C, Abramov A, Baquero AF, Baquero K, Friedrich D, Huard J, Davis R, Kim B, Koch T, Mercer AJ, Misquith A, Murray SA, Perry S, Pino LK, Sanford C, Simon A, Zhang Y, Zipp G, Bizarro CV, Shokhirev MN, Whittle AJ, Searle BC, MacCoss MJ, Saghatelian A, Barnes CA. Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins. Cell Metab 2023; 35:166-183.e11. [PMID: 36599300 PMCID: PMC9889109 DOI: 10.1016/j.cmet.2022.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/19/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023]
Abstract
Microproteins (MPs) are a potentially rich source of uncharacterized metabolic regulators. Here, we use ribosome profiling (Ribo-seq) to curate 3,877 unannotated MP-encoding small ORFs (smORFs) in primary brown, white, and beige mouse adipocytes. Of these, we validated 85 MPs by proteomics, including 33 circulating MPs in mouse plasma. Analyses of MP-encoding mRNAs under different physiological conditions (high-fat diet) revealed that numerous MPs are regulated in adipose tissue in vivo and are co-expressed with established metabolic genes. Furthermore, Ribo-seq provided evidence for the translation of Gm8773, which encodes a secreted MP that is homologous to human and chicken FAM237B. Gm8773 is highly expressed in the arcuate nucleus of the hypothalamus, and intracerebroventricular administration of recombinant mFAM237B showed orexigenic activity in obese mice. Together, these data highlight the value of this adipocyte MP database in identifying MPs with roles in fundamental metabolic and physiological processes such as feeding.
Collapse
Affiliation(s)
- Thomas F Martinez
- Department of Pharmaceutical Sciences, Department of Biological Chemistry, Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | | | - Angie L Bookout
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Eduardo V De Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90616-900, Brazil; Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Cynthia Donaldson
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joan M Vaughan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Calvin Lau
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ariel Abramov
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Arian F Baquero
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Karalee Baquero
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Dave Friedrich
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Justin Huard
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Ray Davis
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Bong Kim
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Ty Koch
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Aaron J Mercer
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Ayesha Misquith
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Sara A Murray
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Sakara Perry
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Lindsay K Pino
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Alex Simon
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Yu Zhang
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Garrett Zipp
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA
| | - Cristiano V Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90616-900, Brazil
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Christopher A Barnes
- Novo Nordisk Research Center Seattle, Inc., Seattle, WA, USA; Velia Therapeutics, Inc., San Diego, CA, USA.
| |
Collapse
|
30
|
Álvarez-Urdiola R, Borràs E, Valverde F, Matus JT, Sabidó E, Riechmann JL. Peptidomics Methods Applied to the Study of Flower Development. Methods Mol Biol 2023; 2686:509-536. [PMID: 37540375 DOI: 10.1007/978-1-0716-3299-4_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Understanding the global and dynamic nature of plant developmental processes requires not only the study of the transcriptome, but also of the proteome, including its largely uncharacterized peptidome fraction. Recent advances in proteomics and high-throughput analyses of translating RNAs (ribosome profiling) have begun to address this issue, evidencing the existence of novel, uncharacterized, and possibly functional peptides. To validate the accumulation in tissues of sORF-encoded polypeptides (SEPs), the basic setup of proteomic analyses (i.e., LC-MS/MS) can be followed. However, the detection of peptides that are small (up to ~100 aa, 6-7 kDa) and novel (i.e., not annotated in reference databases) presents specific challenges that need to be addressed both experimentally and with computational biology resources. Several methods have been developed in recent years to isolate and identify peptides from plant tissues. In this chapter, we outline two different peptide extraction protocols and the subsequent peptide identification by mass spectrometry using the database search or the de novo identification methods.
Collapse
Affiliation(s)
- Raquel Álvarez-Urdiola
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Federico Valverde
- Institute for Plant Biochemistry and Photosynthesis CSIC - University of Seville, Seville, Spain
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - José Luis Riechmann
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| |
Collapse
|
31
|
Averina OA, Permyakov OA, Emelianova MA, Grigoryeva OO, Gulyaev MV, Pavlova OS, Mariasina SS, Frolova OY, Kurkina MV, Baydakova GV, Zakharova EY, Marey MV, Tsarev DA, Tashlitsky VN, Popov VS, Lovat ML, Polshakov VI, Vyssokikh MY, Sergiev PV. Mitochondrial peptide Mtln contributes to oxidative metabolism in mice. Biochimie 2023; 204:136-139. [PMID: 36174793 DOI: 10.1016/j.biochi.2022.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 01/12/2023]
Abstract
Mitoregulin (Mtln) is a recently identified 56 amino acid long mitochondrial peptide conserved in vertebrates. Mtln is known to enhance function of respiratory complex I, which is likely mediated by modulation of lipid composition. To address an influence of Mtln gene on the metabolism we created knockout mice deficient in Mtln gene. In line with accumulation of triglycerides observed earlier on a model of Mtln knockout cell lines, we observed Mtln KO mice to develop obesity on a high fat diet. An increased weight gain could be attributed to enhanced fat accumulation according to the magnetic resonance live imaging. In addition, Mtln KO mice demonstrate elevated serum triglycerides and other oxidation substrates accompanied by an exhaustion of tricarboxylic acids cycle intermediates, suggesting suboptimal oxidation of respiration substrates by mitochondria lacking Mtln.
Collapse
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, Moscow, 119992, 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, Skolkovo, Moscow Region, 143025, Russia
| | - Olga O Grigoryeva
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Mikhail V Gulyaev
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Olga S Pavlova
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Sofia S Mariasina
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992, Moscow, Russia
| | | | - Marina V Kurkina
- Research Centre for Medical Genetics (FSBI, RCMG), 115522, Moscow, Russia
| | - Galina V Baydakova
- Research Centre for Medical Genetics (FSBI, RCMG), 115522, Moscow, Russia
| | | | - Maria V Marey
- Research Center for Obstetrics, Gynecology and Perinatology, 117198, Moscow, Russia
| | | | - Vadim N Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir S Popov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maxim L Lovat
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia; Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia; Institute of Mitoengineering MSU, 119992, Moscow, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Mikhail Yu Vyssokikh
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, 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; Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| |
Collapse
|
32
|
Nabi A, Dilekoglu B, Adebali O, Tastan O. Discovering misannotated lncRNAs using deep learning training dynamics. Bioinformatics 2023; 39:6960922. [PMID: 36571493 PMCID: PMC9825752 DOI: 10.1093/bioinformatics/btac821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 10/05/2022] [Accepted: 12/23/2022] [Indexed: 12/27/2022] Open
Abstract
MOTIVATION Recent experimental evidence has shown that some long non-coding RNAs (lncRNAs) contain small open reading frames (sORFs) that are translated into functional micropeptides, suggesting that these lncRNAs are misannotated as non-coding. Current methods to detect misannotated lncRNAs rely on ribosome-profiling (Ribo-Seq) and mass-spectrometry experiments, which are cell-type dependent and expensive. RESULTS Here, we propose a computational method to identify possible misannotated lncRNAs from sequence information alone. Our approach first builds deep learning models to discriminate coding and non-coding transcripts and leverages these models' training dynamics to identify misannotated lncRNAs-i.e. lncRNAs with coding potential. The set of misannotated lncRNAs we identified significantly overlap with experimentally validated ones and closely resemble coding protein sequences as evidenced by significant BLAST hits. Our analysis on a subset of misannotated lncRNA candidates also shows that some ORFs they contain yield high confidence folded structures as predicted by AlphaFold2. This methodology offers promising potential for assisting experimental efforts in characterizing the hidden proteome encoded by misannotated lncRNAs and for curating better datasets for building coding potential predictors. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/nabiafshan/DetectingMisannotatedLncRNAs. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Afshan Nabi
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Berke Dilekoglu
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Ogun Adebali
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | | |
Collapse
|
33
|
Snoke DB, Mahler CA, Angelotti A, Cole RM, Sparagna GC, Baskin KK, Belury MA. Linoleic Acid-Enriched Diet Increases Mitochondrial Tetralinoleoyl Cardiolipin, OXPHOS Protein Levels, and Uncoupling in Interscapular Brown Adipose Tissue during Diet-Induced Weight Gain. BIOLOGY 2022; 12:9. [PMID: 36671702 PMCID: PMC9854875 DOI: 10.3390/biology12010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/02/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Cardiolipin (CL) is a phospholipid unique to the inner mitochondrial membrane that supports respiratory chain structure and function and is demonstrated to be influenced by types of dietary fats. However, the influence of dietary fat on CL species and how this best supports mitochondrial function in brown adipose tissue (BAT), which exhibits an alternative method of energy utilization through the uncoupling of the mitochondrial proton gradient to generate heat, is not well understood. Therefore, the aim of our study was to evaluate metabolic parameters, interscapular BAT CL quantity, species, and mitochondrial function in mice consuming isocaloric moderate-fat diets with either lard (LD; similar fatty acid profile to western dietary patterns) or safflower oil high in linoleic acid (SO), shown to be metabolically favorable in large clinical meta-analyses. Mice fed the SO diet exhibited decreased adiposity, improved insulin sensitivity, and enrichment of LA-containing CL species in BAT CL. Furthermore, mice fed the SO diet exhibit higher levels of OXPHOS complex proteins and increased oxygen consumption in BAT. Our findings demonstrate that dietary consumption of LA-rich oil improves metabolic parameters, increases LA-containing CL species, and improves BAT function when compared to the consumption of lard in mice during diet-induced weight gain.
Collapse
Affiliation(s)
- Deena B. Snoke
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, OH 43210, USA
| | - Connor A. Mahler
- Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, OH 43210, USA
- Indiana Biosciences Research Institute, Indianapolis, IN 46062, USA
| | - Austin Angelotti
- Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, OH 43210, USA
| | - Rachel M. Cole
- Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, OH 43210, USA
| | - Genevieve C. Sparagna
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kedryn K. Baskin
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Martha A. Belury
- Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
34
|
Yang JE, Zhong WJ, Li JF, Lin YY, Liu FT, Tian H, Chen YJ, Luo XY, Zhuang SM. LINC00998-encoded micropeptide SMIM30 promotes the G1/S transition of cell cycle by regulating cytosolic calcium level. Mol Oncol 2022; 17:901-916. [PMID: 36495128 PMCID: PMC10158777 DOI: 10.1002/1878-0261.13358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/04/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
The biological functions of short open reading frame (sORF)-encoded micropeptides remain largely unknown. Here, we report that LINC00998, a previously annotated lncRNA, was upregulated in multiple cancer types and the sORF on LINC00998 encoded a micropeptide named SMIM30. SMIM30 was localized in the membranes of the endoplasmic reticulum (ER) and mitochondria. Silencing SMIM30 inhibited the proliferation of hepatoma cells in vitro and suppressed the growth of tumor xenografts and N-nitrosodiethylamine-induced hepatoma. Overexpression of the 5'UTR-sORF sequence of LINC00998, encoding wild-type SMIM30, enhanced tumor cell growth, but this was abolished when a premature stop codon was introduced into the sORF via single-base deletion. Gain- and loss-of-function studies revealed that SMIM30 peptide but not LINC00998 reduced cytosolic calcium level, increased CDK4, cyclin E2, phosphorylated-Rb and E2F1, and promoted the G1/S phase transition and cell proliferation. The effect of SMIM30 silencing was attenuated by a calcium chelator or the agonist of sarco/endoplasmic reticulum calcium ATPase (SERCA) pump. These findings suggest a novel function of micropeptide SMIM30 in promoting G1/S transition and cell proliferation by enhancing SERCA activity and reducing cytosolic calcium level.
Collapse
Affiliation(s)
- Jin-E Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wang-Jing Zhong
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jin-Feng Li
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying-Ying Lin
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Feng-Ting Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Tian
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ya-Jing Chen
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Yu Luo
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shi-Mei Zhuang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
35
|
pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation. Nat Commun 2022; 13:6840. [PMID: 36369429 PMCID: PMC9652315 DOI: 10.1038/s41467-022-34529-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
The human transcriptome contains thousands of small open reading frames (sORFs) that encode microproteins whose functions remain largely unexplored. Here, we show that TINCR lncRNA encodes pTINCR, an evolutionary conserved ubiquitin-like protein (UBL) expressed in many epithelia and upregulated upon differentiation and under cellular stress. By gain- and loss-of-function studies, we demonstrate that pTINCR is a key inducer of epithelial differentiation in vitro and in vivo. Interestingly, low expression of TINCR associates with worse prognosis in several epithelial cancers, and pTINCR overexpression reduces malignancy in patient-derived xenografts. At the molecular level, pTINCR binds to SUMO through its SUMO interacting motif (SIM) and to CDC42, a Rho-GTPase critical for actin cytoskeleton remodeling and epithelial differentiation. Moreover, pTINCR increases CDC42 SUMOylation and promotes its activation, triggering a pro-differentiation cascade. Our findings suggest that the microproteome is a source of new regulators of cell identity relevant for cancer.
Collapse
|
36
|
Zheng X, Xiang M. Mitochondrion-located peptides and their pleiotropic physiological functions. FEBS J 2022; 289:6919-6935. [PMID: 35599630 DOI: 10.1111/febs.16532] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 01/13/2023]
Abstract
With the development of advanced technologies, many small open reading frames (sORFs) have been found to be translated into micropeptides. Interestingly, a considerable proportion of micropeptides are located in mitochondria, which are designated here as mitochondrion-located peptides (MLPs). These MLPs often contain a transmembrane domain and show a high degree of conservation across species. They usually act as co-factors of large proteins and play regulatory roles in mitochondria such as electron transport in the respiratory chain, reactive oxygen species (ROS) production, metabolic homeostasis, and so on. Deficiency of MLPs disturbs diverse physiological processes including immunity, differentiation, and metabolism both in vivo and in vitro. These findings reveal crucial functions for MLPs and provide fresh insights into diverse mitochondrion-associated biological processes and diseases.
Collapse
Affiliation(s)
- Xintong Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
37
|
Yu J, Wang W, Yang J, Zhang Y, Gong X, Luo H, Cao N, Xu Z, Tian M, Yang P, Mei Q, Chen Z, Li Z, Li C, Duan X, Lyu QR, Gao C, Zhang B, Wang Y, Wu G, Zeng C. LncRNA PSR Regulates Vascular Remodeling Through Encoding a Novel Protein Arteridin. Circ Res 2022; 131:768-787. [PMID: 36134578 PMCID: PMC9588624 DOI: 10.1161/circresaha.122.321080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
RATIONALE Vascular smooth muscle cells (VSMCs) phenotype switch from contractile to proliferative phenotype is a pathological hallmark in various cardiovascular diseases. Recently, a subset of long noncoding RNAs was identified to produce functional polypeptides. However, the functional impact and regulatory mechanisms of long noncoding RNAs in VSMCs phenotype switching remain to be fully elucidated. OBJECTIVES To illustrate the biological function and mechanism of a VSMC-enriched long noncoding RNA and its encoded peptide in VSMC phenotype switching and vascular remodeling. RESULTS We identified a VSMC-enriched transcript encoded by a previously uncharacterized gene, which we called phenotype switching regulator (PSR), which was markedly upregulated during vascular remodeling. Although PSR was annotated as a long noncoding RNA, we demonstrated that the lncPSR (PSR transcript) also encoded a protein, which we named arteridin. In VSMCs, both arteridin and lncPSR were necessary and sufficient to induce phenotype switching. Mechanistically, arteridin and lncPSR regulate downstream genes by directly interacting with a transcription factor YBX1 (Y-box binding protein 1) and modulating its nuclear translocation and chromatin targeting. Intriguingly, the PSR transcription was also robustly induced by arteridin. More importantly, the loss of PSR gene or arteridin protein significantly attenuated the vascular remodeling induced by carotid arterial injury. In addition, VSMC-specific inhibition of lncPSR using adeno-associated virus attenuated Ang II (angiotensin II)-induced hypertensive vascular remodeling. CONCLUSIONS PSR is a VSMC-enriched gene, and its transcript IncPSR and encoded protein (arteridin) coordinately regulate transcriptional reprogramming through a shared interacting partner, YBX1. This is a previously uncharacterized regulatory circuit in VSMC phenotype switching during vascular remodeling, with lncPSR/arteridin as potential therapeutic targets for the treatment of VSMC phenotype switching-related vascular remodeling.
Collapse
Affiliation(s)
- Junyi Yu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Wei Wang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Jining Yang
- Research Center for Nutrition and Food Safety, Chongqing Key Laboratory of Nutrition and Food Safety, Institute of Military Preventive Medicine, The Third Military Medical University, Chongqing, P.R. China
| | - Ye Zhang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Xue Gong
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Hao Luo
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Nian Cao
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zaicheng Xu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Miao Tian
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Peili Yang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Qiao Mei
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zhi Chen
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zhuxin Li
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Chuanwei Li
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Xudong Duan
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Qing Rex Lyu
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Chen Gao
- Department of Pharmacology & Systems Physiology, University of Cincinnati College of Medicine, OH, USA
| | - Bing Zhang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yibin Wang
- Signature Program in Cardiovascular and Metabolic Diseases, Duke-NUS School of Medicine, Singapore
| | - Gengze Wu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Chunyu Zeng
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China
- Heart Center of Fujian Province, Union Hospital, Fujian Medical University, Fuzhou, P.R. China
- Department of Cardiology, Chongqing General Hospital, Chongqing, P. R. China
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, P.R. China
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing
| |
Collapse
|
38
|
Duffy EE, Finander B, Choi G, Carter AC, Pritisanac I, Alam A, Luria V, Karger A, Phu W, Sherman MA, Assad EG, Pajarillo N, Khitun A, Crouch EE, Ganesh S, Chen J, Berger B, Sestan N, O'Donnell-Luria A, Huang EJ, Griffith EC, Forman-Kay JD, Moses AM, Kalish BT, Greenberg ME. Developmental dynamics of RNA translation in the human brain. Nat Neurosci 2022; 25:1353-1365. [PMID: 36171426 PMCID: PMC10198132 DOI: 10.1038/s41593-022-01164-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 08/12/2022] [Indexed: 01/27/2023]
Abstract
The precise regulation of gene expression is fundamental to neurodevelopment, plasticity and cognitive function. Although several studies have profiled transcription in the developing human brain, there is a gap in understanding of accompanying translational regulation. In this study, we performed ribosome profiling on 73 human prenatal and adult cortex samples. We characterized the translational regulation of annotated open reading frames (ORFs) and identified thousands of previously unknown translation events, including small ORFs that give rise to human-specific and/or brain-specific microproteins, many of which we independently verified using proteomics. Ribosome profiling in stem-cell-derived human neuronal cultures corroborated these findings and revealed that several neuronal activity-induced non-coding RNAs encode previously undescribed microproteins. Physicochemical analysis of brain microproteins identified a class of proteins that contain arginine-glycine-glycine (RGG) repeats and, thus, may be regulators of RNA metabolism. This resource expands the known translational landscape of the human brain and illuminates previously unknown brain-specific protein products.
Collapse
Affiliation(s)
- Erin E Duffy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | | | - GiHun Choi
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ava C Carter
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Iva Pritisanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Aqsa Alam
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA, USA
| | - William Phu
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Maxwell A Sherman
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elena G Assad
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Naomi Pajarillo
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Alexandra Khitun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth E Crouch
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Sanika Ganesh
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jin Chen
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Anne O'Donnell-Luria
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric J Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Pathology Service 113B, San Francisco Veterans Affairs Healthcare System, San Francisco, CA, USA
| | - Eric C Griffith
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Alan M Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Brian T Kalish
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
- Department of Paediatrics, Division of Neonatology, Hospital for Sick Children, Toronto, ON, Canada.
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, ON, Canada.
| | | |
Collapse
|
39
|
Chothani SP, Adami E, Widjaja AA, Langley SR, Viswanathan S, Pua CJ, Zhihao NT, Harmston N, D'Agostino G, Whiffin N, Mao W, Ouyang JF, Lim WW, Lim S, Lee CQE, Grubman A, Chen J, Kovalik JP, Tryggvason K, Polo JM, Ho L, Cook SA, Rackham OJL, Schafer S. A high-resolution map of human RNA translation. Mol Cell 2022; 82:2885-2899.e8. [PMID: 35841888 DOI: 10.1016/j.molcel.2022.06.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 03/10/2022] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome.
Collapse
Affiliation(s)
- Sonia P Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anissa A Widjaja
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Chee Jian Pua
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Nevin Tham Zhihao
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Science Division, Yale-NUS College, Singapore 138527, Singapore
| | - Giuseppe D'Agostino
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nicola Whiffin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Wang Mao
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Wei Wen Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Shiqi Lim
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Cheryl Q E Lee
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - J P Kovalik
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore; London Institute of Medical Sciences, London W12 ONN, UK
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; School of Biological Sciences, University of Southampton, Southampton, UK.
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore.
| |
Collapse
|
40
|
Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
|
41
|
Fu H, Wang T, Kong X, Yan K, Yang Y, Cao J, Yuan Y, Wang N, Kee K, Lu ZJ, Xi Q. A Nodal enhanced micropeptide NEMEP regulates glucose uptake during mesendoderm differentiation of embryonic stem cells. Nat Commun 2022; 13:3984. [PMID: 35810171 PMCID: PMC9271079 DOI: 10.1038/s41467-022-31762-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
TGF-β family proteins including Nodal are known as central regulators of early development in metazoans, yet our understanding of the scope of Nodal signaling’s downstream targets and associated physiological mechanisms in specifying developmentally appropriate cell fates is far from complete. Here, we identified a highly conserved, transmembrane micropeptide—NEMEP—as a direct target of Nodal signaling in mesendoderm differentiation of mouse embryonic stem cells (mESCs), and this micropeptide is essential for mesendoderm differentiation. We showed that NEMEP interacts with the glucose transporters GLUT1/GLUT3 and promotes glucose uptake likely through these interactions. Thus, beyond expanding the scope of known Nodal signaling targets in early development and showing that this target micropeptide augments the glucose uptake during mesendoderm differentiation, our study provides a clear example for the direct functional impact of altered glucose metabolism on cell fate determination. Fu et al. identify the highly conserved, transmembrane micropeptide, NEMEP, as a direct target of Nodal signaling, essential for mesendoderm differentiation. NEMEP interacts with the glucose transporters GLUT1/GLUT3 and promotes glucose uptake.
Collapse
Affiliation(s)
- Haipeng Fu
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tingyu Wang
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaohui Kong
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kun Yan
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yang Yang
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-NIBS, Tsinghua University, Beijing, 100084, China
| | - Jingyi Cao
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yafei Yuan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Nan Wang
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Kehkooi Kee
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zhi John Lu
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Joint Graduate Program of Peking-Tsinghua-NIBS, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
42
|
Liu Y, Zeng S, Wu M. Novel insights into noncanonical open reading frames in cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188755. [PMID: 35777601 DOI: 10.1016/j.bbcan.2022.188755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 12/12/2022]
Abstract
With technological advances, previously neglected noncanonical open reading frames (nORFs) are drawing ever-increasing attention. However, the translation potential of numerous putative nORFs remains elusive, and the functions of noncanonical peptides have not been systemically summarized. Moreover, the relationship between noncanonical peptides and their counterpart protein or RNA products remains elusive and the clinical implementation of noncanonical peptides has not been explored. In this review, we highlight how recent technological advances such as ribosome profiling, bioinformatics approaches and CRISPR/Cas9 facilitate the research of noncanonical peptides. We delineate the features of each nORF category and the evolutionary process underneath the nORFs. Most importantly, we summarize the diversified functions of noncanonical peptides in cancer based on their subcellular location, which reflect their extensive participation in key pathways and essential cellular activities in cancer cells. Meanwhile, the equilibrium between noncanonical peptides and their corresponding transcripts or counterpart products may be dysregulated under pathological states, which is essential for their roles in cancer. Lastly, we explore their underestimated potential in clinical application as diagnostic biomarkers and treatment targets against cancer.
Collapse
Affiliation(s)
- Yihan Liu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan 410008, China; Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Minghua Wu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan, China; The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan 410008, China.
| |
Collapse
|
43
|
Pan J, Wang R, Shang F, Ma R, Rong Y, Zhang Y. Functional Micropeptides Encoded by Long Non-Coding RNAs: A Comprehensive Review. Front Mol Biosci 2022; 9:817517. [PMID: 35769907 PMCID: PMC9234465 DOI: 10.3389/fmolb.2022.817517] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/24/2022] [Indexed: 12/03/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) were originally defined as non-coding RNAs (ncRNAs) which lack protein-coding ability. However, with the emergence of technologies such as ribosome profiling sequencing and ribosome-nascent chain complex sequencing, it has been demonstrated that most lncRNAs have short open reading frames hence the potential to encode functional micropeptides. Such micropeptides have been described to be widely involved in life-sustaining activities in several organisms, such as homeostasis regulation, disease, and tumor occurrence, and development, and morphological development of animals, and plants. In this review, we focus on the latest developments in the field of lncRNA-encoded micropeptides, and describe the relevant computational tools and techniques for micropeptide prediction and identification. This review aims to serve as a reference for future research studies on lncRNA-encoded micropeptides.
Collapse
Affiliation(s)
- Jianfeng Pan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Fangzheng Shang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Rong Ma
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Youjun Rong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
- *Correspondence: Yanjun Zhang,
| |
Collapse
|
44
|
Micropeptides translated from putative long non-coding RNAs. Acta Biochim Biophys Sin (Shanghai) 2022; 54:292-300. [PMID: 35538037 PMCID: PMC9827906 DOI: 10.3724/abbs.2022010] [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] [Indexed: 11/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) transcribed in mammals and eukaryotes were thought to have no protein coding capability. However, recent studies have suggested that plenty of lncRNAs are mis-annotated and virtually contain coding sequences which are translated into functional peptides by ribosomal machinery, and these functional peptides are called micropeptides or small peptides. Here we review the rapidly advancing field of micropeptides translated from putative lncRNAs, describe the strategies for their identification, and elucidate their critical roles in many fundamental biological processes. We also discuss the prospects of research in micropeptides and the potential applications of micropeptides.
Collapse
|
45
|
Xiao MH, Lin YF, Xie PP, Chen HX, Deng JW, Zhang W, Zhao N, Xie C, Meng Y, Liu X, Zhuang SM, Zhu Y, Fang JH. Downregulation of a mitochondrial micropeptide, MPM, promotes hepatoma metastasis by enhancing mitochondrial complex I activity. Mol Ther 2022; 30:714-725. [PMID: 34478872 PMCID: PMC8821931 DOI: 10.1016/j.ymthe.2021.08.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/25/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
We and others have shown that MPM (micropeptide in mitochondria) regulates myogenic differentiation and muscle development. However, the roles of MPM in cancer development remain unknown. Here we revealed that MPM was downregulated significantly in human hepatocellular carcinoma (HCC) tissues and its decrease was associated with increased metastasis potential and HCC recurrence. Gain- and loss-of-function investigations disclosed that in vitro migration/invasion and in vivo liver/lung metastasis of hepatoma cells were repressed by restoring MPM expression and increased by silencing MPM. Mechanism investigations revealed that MPM interacted with NDUFA7. Mitochondrial complex I activity was inhibited by overexpressing MPM and enhanced by siMPM, and this effect of siMPM was attenuated by knocking down NDUFA7. The NAD+/NADH ratio, which was regulated by complex I, was reduced by MPM but increased by siMPM. Treatment with the NAD+ precursor nicotinamide abrogated the inhibitory effect of MPM on hepatoma cell migration. Further investigations showed that miR-17-5p bound to MPM and inhibited MPM expression. miR-17-5p upregulation was associated with MPM downregulation in HCC tissues. These findings indicate that a decrease in MPM expression may promote hepatoma metastasis by increasing mitochondrial complex I activity and the NAD+/NADH ratio.
Collapse
Affiliation(s)
- Man-Huan Xiao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Yi-Fang Lin
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Peng-Peng Xie
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Hua-Xing Chen
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Jun-Wen Deng
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Wei Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Na Zhao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Chen Xie
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Yu Meng
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China
| | - Xingguo Liu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
| | - Shi-Mei Zhuang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China,Corresponding author: Shi-Mei Zhuang, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China.
| | - Ying Zhu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China,Corresponding author: Ying Zhu, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China.
| | - Jian-Hong Fang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China,Corresponding author: Jian-Hong Fang, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Xin Gang Xi Road #135, Guangzhou 510275, P.R. China.
| |
Collapse
|
46
|
Bonilauri B, Dallagiovanna B. Microproteins in skeletal muscle: hidden keys in muscle physiology. J Cachexia Sarcopenia Muscle 2022; 13:100-113. [PMID: 34850602 PMCID: PMC8818594 DOI: 10.1002/jcsm.12866] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022] Open
Abstract
Recent advances in the transcriptomics, translatomics, and proteomics have led us to the exciting new world of functional endogenous microproteins. These microproteins have a small size and are derived from small open reading frames (smORFs) of RNAs previously annotated as non-coding (e.g. lncRNAs and circRNAs) as well as from untranslated regions and canonical mRNAs. The presence of these microproteins reveals a much larger translatable portion of the genome, shifting previously defined dogmas and paradigms. These findings affect our view of organisms as a whole, including skeletal muscle tissue. Emerging evidence demonstrates that several smORF-derived microproteins play crucial roles during muscle development (myogenesis), maintenance, and regeneration, as well as lipid and glucose metabolism and skeletal muscle bioenergetics. These microproteins are also involved in processes including physical activity capacity, cellular stress, and muscular-related diseases (i.e. myopathy, cachexia, atrophy, and muscle wasting). Given the role of these small proteins as important key regulators of several skeletal muscle processes, there are rich prospects for the discovery of new microproteins and possible therapies using synthetic microproteins.
Collapse
Affiliation(s)
- Bernardo Bonilauri
- Laboratory of Basic Biology of Stem Cells (LABCET)Carlos Chagas Institute ‐ Fiocruz‐PRCuritibaParanáBrazil
| | - Bruno Dallagiovanna
- Laboratory of Basic Biology of Stem Cells (LABCET)Carlos Chagas Institute ‐ Fiocruz‐PRCuritibaParanáBrazil
| |
Collapse
|
47
|
The cardiac-enriched microprotein mitolamban regulates mitochondrial respiratory complex assembly and function in mice. Proc Natl Acad Sci U S A 2022; 119:2120476119. [PMID: 35101990 PMCID: PMC8833175 DOI: 10.1073/pnas.2120476119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Microproteins are a growing class of versatile small proteins previously overlooked by standard gene annotation methods due to their small size. Here we characterize mitolamban as a cardiac-enriched inner mitochondrial membrane–localized microprotein, which interacts with complex III of the electron transport chain and contributes to complex III assembly and function. Mitolamban gene deletion in mice leads to a reduction in complex III activity and metabolic perturbations in the heart that are consistent with complex III deficiency, as well as altered complex III assembly into respiratory supercomplexes. These findings define a functional role for mitolamban in the heart and highlight the importance of microproteins in regulating mitochondrial function and cardiomyocyte biology. Emerging evidence indicates that a subset of RNA molecules annotated as noncoding contain short open reading frames that code for small functional proteins called microproteins, which have largely been overlooked due to their small size. To search for cardiac-expressed microproteins, we used a comparative genomics approach and identified mitolamban (Mtlbn) as a highly conserved 47-amino acid transmembrane protein that is abundantly expressed in the heart. Mtlbn localizes specifically to the inner mitochondrial membrane where it interacts with subunits of complex III of the electron transport chain and with mitochondrial respiratory supercomplexes. Genetic deletion of Mtlbn in mice altered complex III assembly dynamics and reduced complex III activity. Unbiased metabolomic analysis of heart tissue from Mtlbn knockout mice further revealed an altered metabolite profile consistent with deficiencies in complex III activity. Cardiac-specific Mtlbn overexpression in transgenic (TG) mice induced cardiomyopathy with histological, biochemical, and ultrastructural pathologic features that contributed to premature death. Metabolomic analysis and biochemical studies indicated that hearts from Mtlbn TG mice exhibited increased oxidative stress and mitochondrial dysfunction. These findings reveal Mtlbn as a cardiac-expressed inner mitochondrial membrane microprotein that contributes to mitochondrial electron transport chain activity through direct association with complex III and the regulation of its assembly and function.
Collapse
|
48
|
Della Bella E, Koch J, Baerenfaller K. Translation and emerging functions of non-coding RNAs in inflammation and immunity. Allergy 2022; 77:2025-2037. [PMID: 35094406 PMCID: PMC9302665 DOI: 10.1111/all.15234] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Regulatory non‐coding RNAs (ncRNAs) including small non‐coding RNAs (sRNAs), long non‐coding RNAs (lncRNAs), and circular RNAs (circRNAs) have gained considerable attention in the last few years. This is mainly due to their condition‐ and tissue‐specific expression and their various modes of action, which suggests them as promising biomarkers and therapeutic targets. One important mechanism of ncRNAs to regulate gene expression is through translation of short open reading frames (sORFs). These sORFs can be located in lncRNAs, in non‐translated regions of mRNAs where upstream ORFs (uORFs) represent the majority, or in circRNAs. Regulation of their translation can function as a quick way to adapt protein production to changing cellular or environmental cues, and can either depend solely on the initiation and elongation of translation, or on the roles of the produced functional peptides. Due to the experimental challenges to pinpoint translation events and to detect the produced peptides, translational regulation through regulatory RNAs is not well studied yet. In the case of circRNAs, they have only recently started to be recognized as regulatory molecules instead of mere artifacts of RNA biosynthesis. Of the many roles described for regulatory ncRNAs, we will focus here on their regulation during inflammation and in immunity.
Collapse
Affiliation(s)
| | - Jana Koch
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Swiss Institute of Bioinformatics (SIB) Davos Switzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Swiss Institute of Bioinformatics (SIB) Davos Switzerland
| |
Collapse
|
49
|
A putative long noncoding RNA-encoded micropeptide maintains cellular homeostasis in pancreatic β cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:307-320. [PMID: 34513312 PMCID: PMC8416971 DOI: 10.1016/j.omtn.2021.06.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 06/30/2021] [Indexed: 12/12/2022]
Abstract
Micropeptides (microproteins) encoded by transcripts previously annotated as long noncoding RNAs (lncRNAs) are emerging as important mediators of fundamental biological processes in health and disease. Here, we applied two computational tools to identify putative micropeptides encoded by lncRNAs that are expressed in the human pancreas. We experimentally verified one such micropeptide encoded by a β cell- and neural cell-enriched lncRNA TCL1 Upstream Neural Differentiation-Associated RNA (TUNAR, also known as TUNA, HI-LNC78, or LINC00617). We named this highly conserved 48-amino-acid micropeptide beta cell- and neural cell-regulin (BNLN). BNLN contains a single-pass transmembrane domain and localizes at the endoplasmic reticulum (ER) in pancreatic β cells. Overexpression of BNLN lowered ER calcium levels, maintained ER homeostasis, and elevated glucose-stimulated insulin secretion in pancreatic β cells. We further assessed the BNLN expression in islets from mice fed a high-fat diet and a regular diet and found that BNLN is suppressed by diet-induced obesity (DIO). Conversely, overexpression of BNLN enhanced insulin secretion in islets from lean and obese mice as well as from humans. Taken together, our study provides the first evidence that lncRNA-encoded micropeptides play a critical role in pancreatic β cell functions and provides a foundation for future comprehensive analyses of micropeptide function and pathophysiological impact on diabetes.
Collapse
|
50
|
Ge Q, Jia D, Cen D, Qi Y, Shi C, Li J, Sang L, Yang LJ, He J, Lin A, Chen S, Wang L. Micropeptide ASAP encoded by LINC00467 promotes colorectal cancer progression by directly modulating ATP synthase activity. J Clin Invest 2021; 131:152911. [PMID: 34591791 DOI: 10.1172/jci152911] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence has shown that open reading frames inside long noncoding RNAs (lncRNAs) could encode micropeptides. However, their roles in cellular energy metabolism and tumor progression remain largely unknown. Here, we identified a 94 amino acid-length micropeptide encoded by lncRNA LINC00467 in colorectal cancer. We also characterized its conservation across higher mammals, localization to mitochondria, and the concerted local functions. This peptide enhanced the ATP synthase construction by interacting with the subunits α and γ (ATP5A and ATP5C), increased ATP synthase activity and mitochondrial oxygen consumption rate, and thereby promoted colorectal cancer cell proliferation. Hence, this micropeptide was termed ATP synthase-associated peptide (ASAP). Furthermore, loss of ASAP suppressed patient-derived xenograft growth with attenuated ATP synthase activity and mitochondrial ATP production. Clinically, high expression of ASAP and LINC00467 predicted poor prognosis of colorectal cancer patients. Taken together, our findings revealed a colorectal cancer-associated micropeptide as a vital player in mitochondrial metabolism and provided a therapeutic target for colorectal cancer.
Collapse
Affiliation(s)
- Qiwei Ge
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.,Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang Province, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Dingjiacheng Jia
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.,Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Dong Cen
- Department of General Surgery and
| | - Yadong Qi
- Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang Province, China.,Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Chengyu Shi
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China
| | - Junhong Li
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China
| | - Lingjie Sang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China
| | - Luo-Jia Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China
| | - Jiamin He
- Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang Province, China.,Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Shujie Chen
- Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang Province, China.,Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang Province, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Liangjing Wang
- Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.,Institution of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang Province, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang Province, China
| |
Collapse
|