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Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. BIOPHYSICAL REPORTS 2024; 4:100167. [PMID: 38909903 DOI: 10.1016/j.bpr.2024.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/09/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. In addition, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from noncoding ones in otherwise ambiguous cases.
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Affiliation(s)
- A M Whited
- BioFrontiers Institute, University of Colorado, Boulder, Colorado
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts
| | - Jeffre Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | | | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts
| | - John L Rinn
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- BioFrontiers Institute, University of Colorado, Boulder, Colorado; Department of Physics, University of Colorado Boulder, Boulder, Colorado.
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2
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Nichols C, Do-Thi VA, Peltier DC. Noncanonical microprotein regulation of immunity. Mol Ther 2024:S1525-0016(24)00324-1. [PMID: 38734902 DOI: 10.1016/j.ymthe.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.
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Affiliation(s)
- Cydney Nichols
- Morris Green Scholars Program, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Van Anh Do-Thi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daniel C Peltier
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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3
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Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589296. [PMID: 38659920 PMCID: PMC11042228 DOI: 10.1101/2024.04.12.589296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. Additionally, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from non-coding ones in otherwise ambiguous cases.
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Affiliation(s)
- A M Whited
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Jeffre Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Biochemistry, University of Colorado Boulder, CO, USA
| | | | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - John L Rinn
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Biochemistry, University of Colorado Boulder, CO, USA
| | - Loren E Hough
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado Boulder, CO, USA
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Zhou H, Wu Y, Cai J, Zhang D, Lan D, Dai X, Liu S, Song T, Wang X, Kong Q, He Z, Tan J, Zhang J. Micropeptides: potential treatment strategies for cancer. Cancer Cell Int 2024; 24:134. [PMID: 38622617 PMCID: PMC11020647 DOI: 10.1186/s12935-024-03281-w] [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: 10/18/2023] [Accepted: 02/23/2024] [Indexed: 04/17/2024] Open
Abstract
Some noncoding RNAs (ncRNAs) carry open reading frames (ORFs) that can be translated into micropeptides, although noncoding RNAs (ncRNAs) have been previously assumed to constitute a class of RNA transcripts without coding capacity. Furthermore, recent studies have revealed that ncRNA-derived micropeptides exhibit regulatory functions in the development of many tumours. Although some of these micropeptides inhibit tumour growth, others promote it. Understanding the role of ncRNA-encoded micropeptides in cancer poses new challenges for cancer research, but also offers promising prospects for cancer therapy. In this review, we summarize the types of ncRNAs that can encode micropeptides, highlighting recent technical developments that have made it easier to research micropeptides, such as ribosome analysis, mass spectrometry, bioinformatics methods, and CRISPR/Cas9. Furthermore, based on the distribution of micropeptides in different subcellular locations, we explain the biological functions of micropeptides in different human cancers and discuss their underestimated potential as diagnostic biomarkers and anticancer therapeutic targets in clinical applications, information that may contribute to the discovery and development of new micropeptide-based tools for early diagnosis and anticancer drug development.
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Affiliation(s)
- He Zhou
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China
| | - Yan Wu
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China
| | - Ji Cai
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China
| | - Dan Zhang
- Zunyi Medical University Library, Zunyi, 563000, China
| | - Dongfeng Lan
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China
| | - Xiaofang Dai
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China
| | - Songpo Liu
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China
| | - Tao Song
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China
| | - Xianyao Wang
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China
| | - Qinghong Kong
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi563000, China
| | - Zhixu He
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, 563000, China.
| | - Jun Tan
- Department of Histology and Embryology, Zunyi Medical University, Zunyi, 563000, China.
| | - Jidong Zhang
- Department of Immunology, Zunyi Medical University, Zunyi City, Guizhou Province, 563000, China.
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi Medical University, Zunyi, 563000, China.
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, 563000, China.
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Tang S, Zhang J, Lou F, Zhou H, Cai X, Wang Z, Sun L, Sun Y, Li X, Fan L, Li Y, Jin X, Deng S, Yin Q, Bai J, Wang H, Wang H. A lncRNA Dleu2-encoded peptide relieves autoimmunity by facilitating Smad3-mediated Treg induction. EMBO Rep 2024; 25:1208-1232. [PMID: 38291338 PMCID: PMC10933344 DOI: 10.1038/s44319-024-00070-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
Micropeptides encoded by short open reading frames (sORFs) within long noncoding RNAs (lncRNAs) are beginning to be discovered and characterized as regulators of biological and pathological processes. Here, we find that lncRNA Dleu2 encodes a 17-amino-acid micropeptide, which we name Dleu2-17aa, that is abundantly expressed in T cells. Dleu2-17aa promotes inducible regulatory T (iTreg) cell generation by interacting with SMAD Family Member 3 (Smad3) and enhancing its binding to the Foxp3 conserved non-coding DNA sequence 1 (CNS1) region. Importantly, the genetic deletion of Dleu2-17aa in mice by start codon mutation impairs iTreg generation and worsens experimental autoimmune encephalomyelitis (EAE). Conversely, the exogenous supplementation of Dleu2-17aa relieves EAE. Our findings demonstrate an indispensable role of Dleu2-17aa in maintaining immune homeostasis and suggest therapeutic applications for this peptide in treating autoimmune diseases.
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Affiliation(s)
- Sibei Tang
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Junxun Zhang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fangzhou Lou
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Hong Zhou
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Xiaojie Cai
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Zhikai Wang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Libo Sun
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Yang Sun
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Xiangxiao Li
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Li Fan
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Yan Li
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Xinping Jin
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Siyu Deng
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Qianqian Yin
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Bai
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China
| | - Hong Wang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Honglin Wang
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201610, China.
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Sahgal A, Uversky V, Davé V. Microproteins transitioning into a new Phase: Defining the undefined. Methods 2023; 220:38-54. [PMID: 37890707 DOI: 10.1016/j.ymeth.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Recent advancements in omics technologies have unveiled a hitherto unknown group of short polypeptides called microproteins (miPs). Despite their size, accumulating evidence has demonstrated that miPs exert varied and potent biological functions. They act in paracrine, juxtracrine, and endocrine fashion, maintaining cellular physiology and driving diseases. The present study focuses on biochemical and biophysical analysis and characterization of twenty-four human miPs using distinct computational methods, including RIDAO, AlphaFold2, D2P2, FuzDrop, STRING, and Emboss Pep wheel. miPs often lack well-defined tertiary structures and may harbor intrinsically disordered regions (IDRs) that play pivotal roles in cellular functions. Our analyses define the physicochemical properties of an essential subset of miPs, elucidating their structural characteristics and demonstrating their propensity for driving or participating in liquid-liquid phase separation (LLPS) and intracellular condensate formation. Notably, miPs such as NoBody and pTUNAR revealed a high propensity for LLPS, implicating their potential involvement in forming membrane-less organelles (MLOs) during intracellular LLPS and condensate formation. The results of our study indicate that miPs have functionally profound implications in cellular compartmentalization and signaling processes essential for regulating normal cellular functions. Taken together, our methodological approach explains and highlights the biological importance of these miPs, providing a deeper understanding of the unusual structural landscape and functionality of these newly defined small proteins. Understanding their functions and biological behavior will aid in developing targeted therapies for diseases that involve miPs.
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Affiliation(s)
- Aayushi Sahgal
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vrushank Davé
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Pathology and Cell Biology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States.
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7
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Jiang Y, Liu Q, Alfredsson L, Klareskog L, Kockum I, Jiang X. A genome-wide cross-trait analysis identifies genomic correlation, pleiotropic loci, and causal relationship between sex hormone-binding globulin and rheumatoid arthritis. Hum Genomics 2023; 17:81. [PMID: 37644603 PMCID: PMC10466838 DOI: 10.1186/s40246-023-00528-x] [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: 06/07/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Our study aims to investigate an intrinsic link underlying sex hormone-binding globulin (SHBG) and rheumatoid arthritis (RA), which remains inconclusive in observational settings. METHODS Summary statistics were collected from the largest GWAS(s) on SHBG adjusted for BMI (SHBGadjBMI; Noverall = 368,929; Nmen = 180,094; Nwomen = 188,908), crude SHBG (Noverall = 370,125; Nmen = 180,726; Nwomen = 189,473), and RA (Ncase = 22,350; Ncontrol = 74,823). A genome-wide cross-trait design was performed to quantify global and local genetic correlation, identify pleiotropic loci, and infer a causal relationship. RESULTS Among the overall population, a significant global genetic correlation was observed for SHBGadjBMI and RA ([Formula: see text] = 0.11, P = 1.0 × 10-4) which was further supported by local signal (1q25.2). A total of 18 independent pleiotropic SNPs were identified, of which three were highly likely causal variants and four were found to have effects on both traits through gene expression mediation. A putative causal association of SHBGadjBMI on RA was demonstrated (OR = 1.20, 95% CI = 1.01-1.43) without evidence of reverse causality (OR = 0.999, 95% CI = 0.997-1.000). Sex-specific analyses revealed distinct shared genetic regions (men: 1q32.1-q32.2 and 5p13.1; women: 1q25.2 and 22q11.21-q11.22) and diverse pleiotropic SNPs (16 in men and 18 in women, nearly half were sex-specific) underlying SHBGadjBMI and RA, demonstrating biological disparities between sexes. Replacing SHBGadjBMI with crude SHBG, a largely similar yet less significant pattern of results was observed. CONCLUSION Our cross-trait analysis suggests an intrinsic, as well as a sex-specific, link underlying SHBG and RA, providing novel insights into disease etiology.
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Affiliation(s)
- Yuan Jiang
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden
| | - Qianwen Liu
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden
| | - Lars Alfredsson
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden
| | - Xia Jiang
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden.
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China.
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Jaiswal M, Kumar S. smAMPsTK: a toolkit to unravel the smORFome encoding AMPs of plant species. J Biomol Struct Dyn 2023:1-13. [PMID: 37464885 DOI: 10.1080/07391102.2023.2235605] [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: 04/07/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
The pervasive repertoire of plant molecules with the potential to serve as a substitute for conventional antibiotics has led to obtaining better insights into plant-derived antimicrobial peptides (AMPs). The massive distribution of Small Open Reading Frames (smORFs) throughout eukaryotic genomes with proven extensive biological functions reflects their practicality as antimicrobials. Here, we have developed a pipeline named smAMPsTK to unveil the underlying hidden smORFs encoding AMPs for plant species. By applying this pipeline, we have elicited AMPs of various functional activity of lengths ranging from 5 to 100 aa by employing publicly available transcriptome data of five different angiosperms. Later, we studied the coding potential of AMPs-smORFs, the inclusion of diverse translation initiation start codons, and amino acid frequency. Codon usage study signifies no such codon usage biases for smORFs encoding AMPs. Majorly three start codons are prominent in generating AMPs. The evolutionary and conservational study proclaimed the widespread distribution of AMPs encoding genes throughout the plant kingdom. Domain analysis revealed that nearly all AMPs have chitin-binding ability, establishing their role as antifungal agents. The current study includes a developed methodology to characterize smORFs encoding AMPs, and their implications as antimicrobial, antibacterial, antifungal, or antiviral provided by SVM score and prediction status calculated by machine learning-based prediction models. The pipeline, complete package, and the results derived for five angiosperms are freely available at https://github.com/skbinfo/smAMPsTK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohini Jaiswal
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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Hassel KR, Brito-Estrada O, Makarewich CA. Microproteins: Overlooked regulators of physiology and disease. iScience 2023; 26:106781. [PMID: 37213226 PMCID: PMC10199267 DOI: 10.1016/j.isci.2023.106781] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Ongoing efforts to generate a complete and accurate annotation of the genome have revealed a significant blind spot for small proteins (<100 amino acids) originating from short open reading frames (sORFs). The recent discovery of numerous sORF-encoded proteins, termed microproteins, that play diverse roles in critical cellular processes has ignited the field of microprotein biology. Large-scale efforts are currently underway to identify sORF-encoded microproteins in diverse cell-types and tissues and specialized methods and tools have been developed to aid in their discovery, validation, and functional characterization. Microproteins that have been identified thus far play important roles in fundamental processes including ion transport, oxidative phosphorylation, and stress signaling. In this review, we discuss the optimized tools available for microprotein discovery and validation, summarize the biological functions of numerous microproteins, outline the promise for developing microproteins as therapeutic targets, and look forward to the future of the field of microprotein biology.
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Affiliation(s)
- Keira R. Hassel
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Omar Brito-Estrada
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Catherine A. Makarewich
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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10
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Inchingolo MA, Diman A, Adamczewski M, Humphreys T, Jaquier-Gubler P, Curran JA. TP53BP1, a dual-coding gene, uses promoter switching and translational reinitiation to express a smORF protein. iScience 2023; 26:106757. [PMID: 37216125 PMCID: PMC10193022 DOI: 10.1016/j.isci.2023.106757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/07/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
The complexity of the metazoan proteome is significantly increased by the expression of small proteins (<100 aa) derived from smORFs within lncRNAs, uORFs, 3' UTRs and, reading frames overlapping the CDS. These smORF encoded proteins (SEPs) have diverse roles, ranging from the regulation of cellular physiological to essential developmental functions. We report the characterization of a new member of this protein family, SEP53BP1, derived from a small internal ORF that overlaps the CDS encoding 53BP1. Its expression is coupled to the utilization of an alternative, cell-type specific promoter coupled to translational reinitiation events mediated by a uORF in the alternative 5' TL of the mRNA. This uORF-mediated reinitiation at an internal ORF is also observed in zebrafish. Interactome studies indicate that the human SEP53BP1 associates with components of the protein turnover pathway including the proteasome, and the TRiC/CCT chaperonin complex, suggesting that it may play a role in cellular proteostasis.
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Affiliation(s)
- Marta A. Inchingolo
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aurélie Diman
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Maxime Adamczewski
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Faculté de Médecine et Pharmacie, Université Grenoble Alpes, Grenoble, France
| | - Tom Humphreys
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Pascale Jaquier-Gubler
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Joseph A. Curran
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
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11
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Pueyo JI, Salazar J, Grincho C, Berni J, Towler BP, Newbury SF. Purriato is a conserved small open reading frame gene that interacts with the CASA pathway to regulate muscle homeostasis and epithelial tissue growth in Drosophila. Front Cell Dev Biol 2023; 11:1117454. [PMID: 36968202 PMCID: PMC10036370 DOI: 10.3389/fcell.2023.1117454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
Recent advances in proteogenomic techniques and bioinformatic pipelines have permitted the detection of thousands of translated small Open Reading Frames (smORFs), which contain less than 100 codons, in eukaryotic genomes. Hundreds of these actively translated smORFs display conserved sequence, structure and evolutionary signatures indicating that the translated peptides could fulfil important biological roles. Despite their abundance, only tens of smORF genes have been fully characterised; these act mainly as regulators of canonical proteins involved in essential cellular processes. Importantly, some of these smORFs display conserved functions with their mutations being associated with pathogenesis. Thus, investigating smORF roles in Drosophila will not only expand our understanding of their functions but it may have an impact in human health. Here we describe the function of a novel and essential Drosophila smORF gene named purriato (prto). prto belongs to an ancient gene family whose members have expanded throughout the Protostomia clade. prto encodes a transmembrane peptide which is localized in endo-lysosomes and perinuclear and plasma membranes. prto is dynamically expressed in mesodermal tissues and imaginal discs. Targeted prto knockdown (KD) in these organs results in changes in nuclear morphology and endo-lysosomal distributions correlating with the loss of sarcomeric homeostasis in muscles and reduction of mitosis in wing discs. Consequently, prto KD mutants display severe reduction of motility, and shorter wings. Finally, our genetic interaction experiments show that prto function is closely associated to the CASA pathway, a conserved mechanism involved in turnover of mis-folded proteins and linked to muscle dystrophies and neurodegenerative diseases. Thus, this study shows the relevance of smORFs in regulating important cellular functions and supports the systematic characterisation of this class of genes to understand their functions and evolution.
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Affiliation(s)
- Jose I. Pueyo
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jorge Salazar
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Carolina Grincho
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jimena Berni
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Benjamin P. Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sarah F. Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
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12
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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.
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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
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13
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Ahangar Davoodi N, Najafi S, Naderi Ghale-Noie Z, Piranviseh A, Mollazadeh S, Ahmadi Asouri S, Asemi Z, Morshedi M, Tamehri Zadeh SS, Hamblin MR, Sheida A, Mirzaei H. Role of non-coding RNAs and exosomal non-coding RNAs in retinoblastoma progression. Front Cell Dev Biol 2022; 10:1065837. [PMID: 36619866 PMCID: PMC9816416 DOI: 10.3389/fcell.2022.1065837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoblastoma (RB) is a rare aggressive intraocular malignancy of childhood that has the potential to affect vision, and can even be fatal in some children. While the tumor can be controlled efficiently at early stages, metastatic tumors lead to high mortality. Non-coding RNAs (ncRNAs) are implicated in a number of physiological cellular process, including differentiation, proliferation, migration, and invasion, The deregulation of ncRNAs is correlated with several diseases, particularly cancer. ncRNAs are categorized into two main groups based on their length, i.e. short and long ncRNAs. Moreover, ncRNA deregulation has been demonstrated to play a role in the pathogenesis and development of RB. Several ncRNAs, such as miR-491-3p, miR-613,and SUSD2 have been found to act as tumor suppressor genes in RB, but other ncRNAs, such as circ-E2F3, NEAT1, and TUG1 act as tumor promoter genes. Understanding the regulatory mechanisms of ncRNAs can provide new opportunities for RB therapy. In the present review, we discuss the functional roles of the most important ncRNAs in RB, their interaction with the genes responsible for RB initiation and progression, and possible future clinical applications as diagnostic and prognostic tools or as therapeutic targets.
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Affiliation(s)
- Nasrin Ahangar Davoodi
- Eye Research Center, Rassoul Akram Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ashkan Piranviseh
- Brain and Spinal Cord Injury Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Sahar Ahmadi Asouri
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammadamin Morshedi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran,School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Amirhossein Sheida
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran,School of Medicine, Kashan University of Medical Sciences, Kashan, Iran,*Correspondence: Amirhossein Sheida, ; Hamed Mirzaei, ,
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran,*Correspondence: Amirhossein Sheida, ; Hamed Mirzaei, ,
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14
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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.
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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
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15
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Translation and natural selection of micropeptides from long non-canonical RNAs. Nat Commun 2022; 13:6515. [PMID: 36316320 PMCID: PMC9622821 DOI: 10.1038/s41467-022-34094-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but lacking canonical coding sequences. Apparently unable to produce peptides, lncRNA function seems to rely only on RNA expression, sequence and structure. Here, we exhaustively detect in-vivo translation of small open reading frames (small ORFs) within lncRNAs using Ribosomal profiling during Drosophila melanogaster embryogenesis. We show that around 30% of lncRNAs contain small ORFs engaged by ribosomes, leading to regulated translation of 100 to 300 micropeptides. We identify lncRNA features that favour translation, such as cistronicity, Kozak sequences, and conservation. For the latter, we develop a bioinformatics pipeline to detect small ORF homologues, and reveal evidence of natural selection favouring the conservation of micropeptide sequence and function across evolution. Our results expand the repertoire of lncRNA biochemical functions, and suggest that lncRNAs give rise to novel coding genes throughout evolution. Since most lncRNAs contain small ORFs with as yet unknown translation potential, we propose to rename them "long non-canonical RNAs".
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16
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Tan HW, Xu YM, Liang ZL, Cai NL, Wu YY, Lau ATY. Single-gene knockout-coupled omics analysis identifies C9orf85 and CXorf38 as two uncharacterized human proteins associated with ZIP8 malfunction. Front Mol Biosci 2022; 9:991308. [PMID: 36330220 PMCID: PMC9623088 DOI: 10.3389/fmolb.2022.991308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/13/2022] [Indexed: 02/05/2023] Open
Abstract
Human transmembrane protein metal cation symporter ZIP8 (SLC39A8) is a member of the solute carrier gene family responsible for intracellular transportation of essential micronutrients, including manganese, selenium, and zinc. Previously, we established a ZIP8-knockout (KO) human cell model using the CRISPR/Cas9 system and explored how the expression of ZIP8 could possibly contribute to a wide range of human diseases. To further assess the biophysiological role of ZIP8, in the current study, we employed isobaric tags for relative and absolute quantitation (iTRAQ) and detected the changes of the proteome in ZIP8-KO cells (proteomic data are available via ProteomeXchange with identifier PXD036680). A total of 286 differentially expressed proteins (206 downregulated and 80 upregulated proteins) were detected in the ZIP8-KO cell model, and subsequent bioinformatics analyses (GO, KEGG, KOG, and PPI) were performed on these proteins. Interestingly, four "uncharacterized" proteins (proteins with unknown biological function) were identified in the differentially expressed proteins: C1orf198, C9orf85, C17orf75, and CXorf38-all of which were under-expressed in the ZIP8-KO cells. Notably, C9orf85 and CXorf38 were amongst the top-10 most downregulated proteins, and their expressions could be selectively induced by essential micronutrients. Furthermore, clinical-based bioinformatic analysis indicated that positive correlations between the gene expressions of ZIP8 and C9orf85 or CXorf38 were observed in multiple cancer types. Overall, this study reveals the proteomic landscape of cells with impaired ZIP8 and uncovers the potential relationships between essential micronutrients and uncharacterized proteins C9orf85 and CXorf38. The differentially expressed proteins identified in ZIP8-KO cells could be the potential targets for diagnosing and/or treating human ZIP8-associated diseases, including but not limited to malnutrition, viral infection, and cancers.
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Affiliation(s)
- Heng Wee Tan
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, China
| | | | | | | | | | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, China
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17
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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.
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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.
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18
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Abstract
In eukaryotic organisms, noncoding RNAs (ncRNAs) have been implicated as important regulators of multifaceted biological processes, including transcriptional, posttranscriptional, and epigenetic regulation of gene expression. In recent years, it is becoming clear that protozoan parasites encode diverse ncRNA transcripts; however, little is known about their cellular functions. Recent advances in high-throughput “omic” studies identified many novel long ncRNAs (lncRNAs) in apicomplexan parasites, some of which undergo splicing, polyadenylation, and encode small proteins. To date, only a few of them are characterized, leaving a big gap in our understanding regarding their origin, mode of action, and functions in parasite biology. In this review, we focus on lncRNAs of the human malaria parasite Plasmodium falciparum and highlight their cellular functions and possible mechanisms of action.
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Affiliation(s)
- Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail:
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19
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Zhang Z, Li Y, Yuan W, Wang Z, Wan C. Proteomic-driven identification of short open reading frame-encoded peptides. Proteomics 2022; 22:e2100312. [PMID: 35384297 DOI: 10.1002/pmic.202100312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022]
Abstract
Accumulating evidence has shown that a large number of short open reading frames (sORFs) also have the ability to encode proteins. The discovery of sORFs opens up a new research area, leading to the identification and functional study of sORF encoded peptides (SEPs) at the omics level. Besides bioinformatics prediction and ribosomal profiling, mass spectrometry (MS) has become a significant tool as it directly detects the sequence of SEPs. Though MS-based proteomics methods have proved to be effective for qualitative and quantitative analysis of SEPs, the detection of SEPs is still a great challenge due to their low abundance and short sequence. To illustrate the progress in method development, we described and discussed the main steps of large-scale proteomics identification of SEPs, including SEP extraction and enrichment, MS detection, data processing and quality control, quantification, and function prediction and validation methods. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zheng Zhang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Yujie Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Wenqian Yuan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Zhiwei Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
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20
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The microprotein Nrs1 rewires the G1/S transcriptional machinery during nitrogen limitation in budding yeast. PLoS Biol 2022; 20:e3001548. [PMID: 35239649 PMCID: PMC8893695 DOI: 10.1371/journal.pbio.3001548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/19/2022] [Indexed: 12/01/2022] Open
Abstract
Commitment to cell division at the end of G1 phase, termed Start in the budding yeast Saccharomyces cerevisiae, is strongly influenced by nutrient availability. To identify new dominant activators of Start that might operate under different nutrient conditions, we screened a genome-wide ORF overexpression library for genes that bypass a Start arrest caused by absence of the G1 cyclin Cln3 and the transcriptional activator Bck2. We recovered a hypothetical gene YLR053c, renamed NRS1 for Nitrogen-Responsive Start regulator 1, which encodes a poorly characterized 108 amino acid microprotein. Endogenous Nrs1 was nuclear-localized, restricted to poor nitrogen conditions, induced upon TORC1 inhibition, and cell cycle-regulated with a peak at Start. NRS1 interacted genetically with SWI4 and SWI6, which encode subunits of the main G1/S transcription factor complex SBF. Correspondingly, Nrs1 physically interacted with Swi4 and Swi6 and was localized to G1/S promoter DNA. Nrs1 exhibited inherent transactivation activity, and fusion of Nrs1 to the SBF inhibitor Whi5 was sufficient to suppress other Start defects. Nrs1 appears to be a recently evolved microprotein that rewires the G1/S transcriptional machinery under poor nitrogen conditions. Commitment to cell division at the end of G1 phase in the budding yeast Saccharomyces cerevisiae is strongly influenced by nutrient availability. This study identifies a micro-protein that promotes G1/S transcription activation and cell cycle entry in yeast under nitrogen-limited conditions.
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21
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Wang Z, Pan N, Yan J, Wan J, Wan C. Systematic Identification of Microproteins during the Development of Drosophila melanogaster. J Proteome Res 2022; 21:1114-1123. [PMID: 35227063 DOI: 10.1021/acs.jproteome.2c00004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Short open reading frame-encoded peptides (SEPs) are microproteins with less than 100 amino acids that play an essential role in the growth and development of organisms. There are plenty of short open reading frames in Drosophila melanogaster that potentially code polypeptides. We chose 11 time points during the life cycle of Drosophila to investigate microproteins, particularly those related to development. Finally, we identified a total of 410 microproteins, of which 27 were noncoding RNA-encoded proteins. Of the 410 microproteins, 74 were expressed in all stages from embryo to adults, whereas 300 microproteins were only found in one or two time points. Approximately, one-third of the microproteins were not reported previously and 44 were obtained from de novo sequencing, validated by synthetic peptides. These microproteins are related to the main bioprocesses of growth and development, such as multicellular organism reproduction, postmating behavior, and oviposition. Over half of the microproteins have predicted functional domains and are conserved across species, suggesting that these microproteins have critical functions in fly development. This work enriches the D. melanogaster proteome and provides a significant data resource for growth and development research.
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Affiliation(s)
- Zhiwei Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Ni Pan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Jiahao Yan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Jian Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
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22
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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.
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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
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23
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Magny EG, Platero AI, Bishop SA, Pueyo JI, Aguilar-Hidalgo D, Couso JP. Pegasus, a small extracellular peptide enhancing short-range diffusion of Wingless. Nat Commun 2021; 12:5660. [PMID: 34580289 PMCID: PMC8476528 DOI: 10.1038/s41467-021-25785-z] [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: 05/18/2020] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
Small Open Reading Frames (smORFs) coding for peptides of less than 100 amino-acids are an enigmatic and pervasive gene class, found in the tens of thousands in metazoan genomes. Here we reveal a short 80 amino-acid peptide (Pegasus) which enhances Wingless/Wnt1 protein short-range diffusion and signalling. During Drosophila wing development, Wingless has sequential functions, including late induction of proneural gene expression and wing margin development. Pegasus mutants produce wing margin defects and proneural expression loss similar to those of Wingless. Pegasus is secreted, and co-localizes and co-immunoprecipitates with Wingless, suggesting their physical interaction. Finally, measurements of fixed and in-vivo Wingless gradients support that Pegasus increases Wingless diffusion in order to enhance its signalling. Our results unveil a new element in Wingless signalling and clarify the patterning role of Wingless diffusion, while corroborating the link between small open reading frame peptides, and regulation of known proteins with membrane-related functions.
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Affiliation(s)
- Emile G Magny
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Ana Isabel Platero
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Sarah A Bishop
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide, Sevilla, Spain.,Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Jose I Pueyo
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Daniel Aguilar-Hidalgo
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Juan Pablo Couso
- Centro Andaluz de Biologia del Desarrollo, CSIC-Universidad Pablo de Olavide, Sevilla, Spain.
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24
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Guerra-Almeida D, Tschoeke DA, da-Fonseca RN. Understanding small ORF diversity through a comprehensive transcription feature classification. DNA Res 2021; 28:6317669. [PMID: 34240112 PMCID: PMC8435553 DOI: 10.1093/dnares/dsab007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Small open reading frames (small ORFs/sORFs/smORFs) are potentially coding sequences smaller than 100 codons that have historically been considered junk DNA by gene prediction software and in annotation screening; however, the advent of next-generation sequencing has contributed to the deeper investigation of junk DNA regions and their transcription products, resulting in the emergence of smORFs as a new focus of interest in systems biology. Several smORF peptides were recently reported in noncanonical mRNAs as new players in numerous biological contexts; however, their relevance is still overlooked in coding potential analysis. Hence, this review proposes a smORF classification based on transcriptional features, discussing the most promising approaches to investigate smORFs based on their different characteristics. First, smORFs were divided into nonexpressed (intergenic) and expressed (genic) smORFs. Second, genic smORFs were classified as smORFs located in noncoding RNAs (ncRNAs) or canonical mRNAs. Finally, smORFs in ncRNAs were further subdivided into sequences located in small or long RNAs, whereas smORFs located in canonical mRNAs were subdivided into several specific classes depending on their localization along the gene. We hope that this review provides new insights into large-scale annotations and reinforces the role of smORFs as essential components of a hidden coding DNA world.
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Affiliation(s)
- Diego Guerra-Almeida
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diogo Antonio Tschoeke
- Alberto Luiz Coimbra Institute of Graduate Studies and Engineering Research (COPPE), Biomedical Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo Nunes- da-Fonseca
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
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25
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Immarigeon C, Frei Y, Delbare SYN, Gligorov D, Machado Almeida P, Grey J, Fabbro L, Nagoshi E, Billeter JC, Wolfner MF, Karch F, Maeda RK. Identification of a micropeptide and multiple secondary cell genes that modulate Drosophila male reproductive success. Proc Natl Acad Sci U S A 2021; 118:e2001897118. [PMID: 33876742 PMCID: PMC8053986 DOI: 10.1073/pnas.2001897118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Even in well-characterized genomes, many transcripts are considered noncoding RNAs (ncRNAs) simply due to the absence of large open reading frames (ORFs). However, it is now becoming clear that many small ORFs (smORFs) produce peptides with important biological functions. In the process of characterizing the ribosome-bound transcriptome of an important cell type of the seminal fluid-producing accessory gland of Drosophila melanogaster, we detected an RNA, previously thought to be noncoding, called male-specific abdominal (msa). Notably, msa is nested in the HOX gene cluster of the Bithorax complex and is known to contain a micro-RNA within one of its introns. We find that this RNA encodes a "micropeptide" (9 or 20 amino acids, MSAmiP) that is expressed exclusively in the secondary cells of the male accessory gland, where it seems to accumulate in nuclei. Importantly, loss of function of this micropeptide causes defects in sperm competition. In addition to bringing insights into the biology of a rare cell type, this work underlines the importance of small peptides, a class of molecules that is now emerging as important actors in complex biological processes.
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Affiliation(s)
- Clément Immarigeon
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland;
| | - Yohan Frei
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Sofie Y N Delbare
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - Dragan Gligorov
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Pedro Machado Almeida
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jasmine Grey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - Léa Fabbro
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Emi Nagoshi
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jean-Christophe Billeter
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9700 CC, The Netherlands
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703
| | - François Karch
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland
| | - Robert K Maeda
- Department of Genetics and Evolution, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland;
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26
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Schlesinger D, Elsässer SJ. Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins. FEBS J 2021; 289:53-74. [PMID: 33595896 DOI: 10.1111/febs.15769] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/17/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023]
Abstract
Short ORFs (sORFs), that is, occurrences of a start and stop codon within 100 codons or less, can be found in organisms of all domains of life, outnumbering annotated protein-coding ORFs by orders of magnitude. Even though functional proteins smaller than 100 amino acids are known, the coding potential of sORFs has often been overlooked, as it is not trivial to predict and test for functionality within the large number of sORFs. Recent advances in ribosome profiling and mass spectrometry approaches, together with refined bioinformatic predictions, have enabled a huge leap forward in this field and identified thousands of likely coding sORFs. A relatively low number of small proteins or microproteins produced from these sORFs have been characterized so far on the molecular, structural, and/or mechanistic level. These however display versatile and, in some cases, essential cellular functions, allowing for the exciting possibility that many more, previously unknown small proteins might be encoded in the genome, waiting to be discovered. This review will give an overview of the steadily growing microprotein field, focusing on eukaryotic small proteins. We will discuss emerging themes in the molecular action of microproteins, as well as advances and challenges in microprotein identification and characterization.
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Affiliation(s)
- Dörte Schlesinger
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
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27
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Nasir MA, Nawaz S, Huang J. A Mini-review of Computational Approaches to Predict Functions and Findings of Novel Micro Peptides. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200811130522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
:
New techniques in bioinformatics and the study of the transcriptome at a wide-scale
have uncovered the fact that a large part of the genome is being translated than recently perceived
thoughts and research, bringing about the creation of a various quantity of RNA with proteincoding
and noncoding potential. A lot of RNA particles have been considered as noncoding due to
many reasons, according to developing proofs. Like many sORFs that encode many functional
micro peptides have neglected due to their tiny sizes.
:
Advanced studies reveal many major biological functions of these sORFs and their encoded micro
peptides in a different and wide range of species. All the achievement in the identification of these
sORFs and micro peptides is due to the progressive bioinformatics and high-throughput
sequencing methods. This field has pulled in more consideration due to the detection of a large
number of more sORFs and micro peptides. Nowadays, COVID-19 grabs all the attention of
science as it is a sudden outbreak. sORFs of COVID-19 should be revealed for new ways to
understand this virus. This review discusses ongoing progress in the systems for the identification
and distinguishing proof of sORFs and micro peptides.
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Affiliation(s)
- Mohsin Ali Nasir
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Samia Nawaz
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
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28
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Neville MDC, Kohze R, Erady C, Meena N, Hayden M, Cooper DN, Mort M, Prabakaran S. A platform for curated products from novel open reading frames prompts reinterpretation of disease variants. Genome Res 2021; 31:327-336. [PMID: 33468550 PMCID: PMC7849405 DOI: 10.1101/gr.263202.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022]
Abstract
Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in diverse regions of the genome, including in long noncoding RNAs, pseudogenes, 3' UTRs, 5' UTRs, and alternative reading frames of canonical protein coding exons. There is therefore a pressing need to evaluate the potential functional importance of these unannotated transcripts and proteins in biological pathways and human disease on a larger scale, rather than one at a time. In this study, we outline the creation of a valuable nORFs data set with experimental evidence of translation for the community, use measures of heritability and selection that reveal signals for functional importance, and show the potential implications for functional interpretation of genetic variants in nORFs. Our results indicate that some variants that were previously classified as being benign or of uncertain significance may have to be reinterpreted.
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Affiliation(s)
- Matthew D C Neville
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Robin Kohze
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Chaitanya Erady
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Narendra Meena
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Matthew Hayden
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Sudhakaran Prabakaran
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
- St Edmund's College, University of Cambridge, Cambridge CB3 0BN, United Kingdom
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29
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Erady C, Boxall A, Puntambekar S, Suhas Jagannathan N, Chauhan R, Chong D, Meena N, Kulkarni A, Kasabe B, Prathivadi Bhayankaram K, Umrania Y, Andreani A, Nel J, Wayland MT, Pina C, Lilley KS, Prabakaran S. Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions. NPJ Genom Med 2021; 6:4. [PMID: 33495453 PMCID: PMC7835362 DOI: 10.1038/s41525-020-00167-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022] Open
Abstract
Uncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.
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Affiliation(s)
- Chaitanya Erady
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Adam Boxall
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Shraddha Puntambekar
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - N Suhas Jagannathan
- Cancer and Stem Cell Biology Programme, and Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Ruchi Chauhan
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - David Chong
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Narendra Meena
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Apurv Kulkarni
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Bhagyashri Kasabe
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | | | - Yagnesh Umrania
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Adam Andreani
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Jean Nel
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Matthew T Wayland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Cristina Pina
- Department of Haematology, Cambridge Biomedical Campus, Cambridge, CB2 0PT, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Sudhakaran Prabakaran
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK.
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30
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Decio P, Ustaoglu P, Derecka K, Hardy ICW, Roat TC, Malaspina O, Mongan N, Stöger R, Soller M. Thiamethoxam exposure deregulates short ORF gene expression in the honey bee and compromises immune response to bacteria. Sci Rep 2021; 11:1489. [PMID: 33452318 PMCID: PMC7811001 DOI: 10.1038/s41598-020-80620-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 12/23/2020] [Indexed: 01/29/2023] Open
Abstract
Maximizing crop yields relies on the use of agrochemicals to control insect pests. One of the most widely used classes of insecticides are neonicotinoids that interfere with signalling of the neurotransmitter acetylcholine, but these can also disrupt crop-pollination services provided by bees. Here, we analysed whether chronic low dose long-term exposure to the neonicotinoid thiamethoxam alters gene expression and alternative splicing in brains of Africanized honey bees, Apis mellifera, as adaptation to altered neuronal signalling. We find differentially regulated genes that show concentration-dependent responses to thiamethoxam, but no changes in alternative splicing. Most differentially expressed genes have no annotated function but encode short Open Reading Frames, a characteristic feature of anti-microbial peptides. As this suggested that immune responses may be compromised by thiamethoxam exposure, we tested the impact of thiamethoxam on bee immunity by injecting bacteria. We show that intrinsically sub-lethal thiamethoxam exposure makes bees more vulnerable to normally non-pathogenic bacteria. Our findings imply a synergistic mechanism for the observed bee population declines that concern agriculturists, conservation ecologists and the public.
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Affiliation(s)
- Pâmela Decio
- grid.410543.70000 0001 2188 478XInstitute of Biosciences, São Paulo State University (Unesp), Rio Claro, Brazil
| | - Pinar Ustaoglu
- grid.6572.60000 0004 1936 7486School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Kamila Derecka
- grid.4563.40000 0004 1936 8868School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Ian C. W. Hardy
- grid.4563.40000 0004 1936 8868School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Thaisa C. Roat
- grid.410543.70000 0001 2188 478XInstitute of Biosciences, São Paulo State University (Unesp), Rio Claro, Brazil
| | - Osmar Malaspina
- grid.410543.70000 0001 2188 478XInstitute of Biosciences, São Paulo State University (Unesp), Rio Claro, Brazil
| | - Nigel Mongan
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Reinhard Stöger
- grid.4563.40000 0004 1936 8868School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Matthias Soller
- grid.6572.60000 0004 1936 7486School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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31
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Chen Y, Ho L, Tergaonkar V. sORF-Encoded MicroPeptides: New players in inflammation, metabolism, and precision medicine. Cancer Lett 2020; 500:263-270. [PMID: 33157158 DOI: 10.1016/j.canlet.2020.10.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 12/30/2022]
Abstract
Significant technological advances have enabled the discovery and identification of a new class of molecules, micropeptides or small ORF encoded peptides (SEPs) within non-coding RNAs (ncRNAs). As ncRNAs are well known to be transcriptionally silent, the discovery of SEPs implies that many ncRNAs are misannotated or play both coding and non-coding functions. SEPs have reportedly diverse regulatory roles in embryogenesis, myogenesis, inflammation, diseases, and cancer. SEPs appearing in different subcellular compartments show distinct functions. In this review, we summarized the functions of SEPs that have been characterized thus far. As SEPs are amenable to therapeutic development as biologics, understanding their underlying functions will provide novel targets for the treatment of inflammatory or metabolic disorders.
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Affiliation(s)
- Ying Chen
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore.
| | - Lena Ho
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore; Cardiovascular Metabolic Disorders Program, Duke-NUS Graduate School, Singapore; Institute of Medical Biology, A*STAR, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore; Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117597, Singapore.
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32
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Hu Y, Zhao M, Li L, Ding J, Gui YM, Wei TW. miR-491-3p is Downregulated in Retinoblastoma and Inhibit Tumor Cells Growth and Metastasis by Targeting SNN. Biochem Genet 2020; 59:453-474. [PMID: 33098307 PMCID: PMC7946698 DOI: 10.1007/s10528-020-10007-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023]
Abstract
Retinoblastoma (Rb) is the most common pediatric malignant tumor of the eyes. Previous studies demonstrated that miR-491-3p is downregulated in various cancers. However, its function in Rb remains unknown. A total of 15 pairs of primary Rb tissues and adjacent noncancerous tissues were collected. Quantitative real-time PCR (qRT-PCR) was used to investigate the expression profiles of miR-491-3p. qRT-PCR, western blotting and in situ immunocytochemistry were performed to investigate the expression profiles of epithelial–mesenchymal transition-related proteins (E-cadherin, Vimentin and N-cadherin) in Rb tissues and Rb cell lines as well as cell morphology. Cell proliferation was estimated by MTS and colony formation assays. Apoptosis was determined by FACS, cell migration and invasion were analyzed using transwell chambers. MiR-491-3p’s target genes were predicted using target gene prediction databases. The interplay between miR-491-3p and SNN was evaluated through dual luciferase reporter gene assay. MiR-491-3p was significantly downregulated in mixed collection of 15 pairs of Rb tissues and Rb cell lines. Overexpression of miR-491-3p enhanced apoptosis, and significantly suppressed proliferation, migration and invasion of Rb cells. In contrast, the present of miR-491-3p inhibitor showed reversed results which apoptosis decreased, while cell proliferation of ARPE-19 cells increased. In addition, miR-491-3p increased the expression of E-cadherin, and dramatically decreased the expression of Vimentin and N-cadherin in Rb tissues and Rb cell lines, noticeable changes in morphology, too, as cells became less cohesive and more adhering. We found out that SNN was the pairing target of miR-491-3p and result showed that miR-491-3p and SNN interacted with each other. We also found out that the effects of miR-491-3p were in Rb cells were almost entirely canceled out at the overexpression of SNN. Our findings collectively suggest that miR-491-3p is an important tumor suppressor in Rb, which inhibits tumor growth and metastasis in Rb. These implicate it may be explored as a new therapeutic target in Rb.
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Affiliation(s)
- Yang Hu
- Department of Ophthalmology, Puren Hospital of Wuhan University of Science and Technology, No.1 Benxi Road, Qingshan District, Wuhan, 430080, Hubei Province, People's Republic of China.
| | - Ming Zhao
- Department of Ophthalmology, Puren Hospital of Wuhan University of Science and Technology, No.1 Benxi Road, Qingshan District, Wuhan, 430080, Hubei Province, People's Republic of China
| | - Li Li
- Department of Ophthalmology, Puren Hospital of Wuhan University of Science and Technology, No.1 Benxi Road, Qingshan District, Wuhan, 430080, Hubei Province, People's Republic of China
| | - Jie Ding
- Department of Ophthalmology, Puren Hospital of Wuhan University of Science and Technology, No.1 Benxi Road, Qingshan District, Wuhan, 430080, Hubei Province, People's Republic of China
| | - Yu-Min Gui
- Department of Ophthalmology, Puren Hospital of Wuhan University of Science and Technology, No.1 Benxi Road, Qingshan District, Wuhan, 430080, Hubei Province, People's Republic of China
| | - Tan-Wei Wei
- Department of Ophthalmology, Puren Hospital of Wuhan University of Science and Technology, No.1 Benxi Road, Qingshan District, Wuhan, 430080, Hubei Province, People's Republic of China
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33
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Patraquim P, Mumtaz MAS, Pueyo JI, Aspden JL, Couso JP. Developmental regulation of canonical and small ORF translation from mRNAs. Genome Biol 2020; 21:128. [PMID: 32471506 PMCID: PMC7260771 DOI: 10.1186/s13059-020-02011-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation of many genes. Here we present an improved version of Poly-Ribo-Seq and apply it to Drosophila melanogaster embryos to extend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis. RESULTS We obtain highly correlated samples across five embryonic stages, with nearly 500 million putative ribosomal footprints mapped to mRNAs, and compare them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time in Drosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation. We propose a simple binomial probability metric to ascertain translation probability. Our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5' mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal-to zygotic transition. CONCLUSIONS We suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding and to defective ribosomal scanning of ORFs outside periods of productive translation. Our results are compatible with the main function of upstream short ORFs being to buffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evolutionary transitory state towards full coding function.
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Affiliation(s)
- Pedro Patraquim
- Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain
| | | | | | - Julie Louise Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Juan-Pablo Couso
- Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain. .,Previous address: Brighton and Sussex Medical School, Brighton, East Sussex, UK.
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34
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Abstract
Recent advancements in genetic and proteomic technologies have revealed that more of the genome encodes proteins than originally thought possible. Specifically, some putative long noncoding RNAs (lncRNAs) have been misannotated as noncoding. Numerous lncRNAs have been found to contain short open reading frames (sORFs) which have been overlooked because of their small size. Many of these sORFs encode small proteins or micropeptides with fundamental biological importance. These micropeptides can aid in diverse processes, including cell division, transcription regulation, and cell signaling. Here we discuss strategies for establishing the coding potential of putative lncRNAs and describe various functions of known micropeptides.
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35
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Makarewich CA. The hidden world of membrane microproteins. Exp Cell Res 2020; 388:111853. [PMID: 31978386 DOI: 10.1016/j.yexcr.2020.111853] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/03/2020] [Accepted: 01/14/2020] [Indexed: 12/26/2022]
Abstract
Proteins are critical components of biological membranes and play key roles in many essential cellular processes. Membrane proteins are a structurally and functionally diverse family of proteins that have recently expanded to include a number of newly discovered tiny proteins called microproteins, or micropeptides. These microproteins are generated from small open reading frames, which produce protein products that are less than 100 amino acids in length. While not all microproteins are membrane proteins, this review will focus specifically on this subclass to highlight some of the important biological activities that have been ascribed to these molecules and to emphasize their promise as exciting new players in membrane biology.
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Affiliation(s)
- Catherine A Makarewich
- The Heart Institute and Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
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36
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Tobias-Santos V, Guerra-Almeida D, Mury F, Ribeiro L, Berni M, Araujo H, Logullo C, Feitosa NM, de Souza-Menezes J, Pessoa Costa E, Nunes-da-Fonseca R. Multiple Roles of the Polycistronic Gene Tarsal-less/Mille-Pattes/Polished-Rice During Embryogenesis of the Kissing Bug Rhodnius prolixus. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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Zheng GZ, Li W, Liu ZY. Alternative role of noncoding RNAs: coding and noncoding properties. J Zhejiang Univ Sci B 2019; 20:920-927. [PMID: 31595728 DOI: 10.1631/jzus.b1900336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Noncoding RNAs (ncRNAs) have played a critical role in cellular biological functions. Recently, some peptides or proteins originating from annotated ncRNAs were identified in organism development and various diseases. Here, we briefly review several novel peptides translated by annotated ncRNAs and related key functions. In addition, we summarize the potential mechanism of bifunctional ncRNAs and propose a specific "switch" triggering the transformation from the noncoding to the coding state under certain stimuli or cellular stress. The coding properties of ncRNAs and their peptide products may provide a novel horizon in proteomic research and can be regarded as a potential therapeutic target for the treatment of various diseases.
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Affiliation(s)
- Gui-Zhen Zheng
- Department of Emergency Internal Medicine, Shanghai East Hospital, Tongji University, Shanghai 200120, China
| | - Wei Li
- Department of General Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Zhi-Yong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China.,Kunming General Hospital of Chengdu Military Command, Kunming 650032, China
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38
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Ruiz-Orera J, Albà MM. Conserved regions in long non-coding RNAs contain abundant translation and protein-RNA interaction signatures. NAR Genom Bioinform 2019; 1:e2. [PMID: 33575549 PMCID: PMC7671363 DOI: 10.1093/nargab/lqz002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/14/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
The mammalian transcriptome includes thousands of transcripts that do not correspond to annotated protein-coding genes and that are known as long non-coding RNAs (lncRNAs). A handful of lncRNAs have well-characterized regulatory functions but the biological significance of the majority of them is not well understood. LncRNAs that are conserved between mice and humans are likely to be enriched in functional sequences. Here, we investigate the presence of different types of ribosome profiling signatures in lncRNAs and how they relate to sequence conservation. We find that lncRNA-conserved regions contain three times more ORFs with translation evidence than non-conserved ones, and identify nine cases that display significant sequence constraints at the amino acid sequence level. The study also reveals that conserved regions in intergenic lncRNAs are significantly enriched in protein–RNA interaction signatures when compared to non-conserved ones; this includes sites in well-characterized lncRNAs, such as Cyrano, Malat1, Neat1 and Meg3, as well as in tens of lncRNAs of unknown function. This work illustrates how the analysis of ribosome profiling data coupled with evolutionary analysis provides new opportunities to explore the lncRNA functional landscape.
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Affiliation(s)
- Jorge Ruiz-Orera
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, Dr Aiguader 88, Barcelona 08003, Spain
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, Dr Aiguader 88, Barcelona 08003, Spain.,Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, Barcelona 08010, Spain
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39
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Gulluni F, De Santis MC, Margaria JP, Martini M, Hirsch E. Class II PI3K Functions in Cell Biology and Disease. Trends Cell Biol 2019; 29:339-359. [DOI: 10.1016/j.tcb.2019.01.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022]
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40
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Abstract
INTRODUCTION Small open reading frames (sORFs) with potential protein-coding capacity have been disclosed in various transcripts, including long noncoding RNAs (LncRNAs), mRNAs (5'-upstream, coding domain, and 3'-downstream), circular RNAs, pri-miRNAs, and ribosomal RNAs (rRNAs). Recent characterization of several sORF-encoded peptides (SEPs or micropeptides) revealed their important roles in many fundamental biological processes in a broad range of species from yeast to human. The success in the mining of micropeptides attributes to the advanced bioinformatics and high-throughput sequencing techniques. Areas covered: sORFs and SEPs were overlooked for their tiny size and the difficulty of identification by bioinformatics analyses. With more and more sORFs and SEPs have been identified, this field has attracted more attention. This review covers recent advances in the strategies for the detection and identification of sORFs and SEPs. Expert commentary: The advantages and drawbacks of the strategies for detection and identification of sORFs and SEPs are discussed, as well as the techniques that are used to decipher the roles of micropeptides in organisms are described.
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Affiliation(s)
- Xinqiang Yin
- a The Engineering Research Center of Synthetic Polypeptide Drug Discovery and Evaluation of Jiangsu Province , China Pharmaceutical University , Nanjing , China.,b The Basic Medical School , North Sichuan Medical College , Nanchong , China
| | - Yuanyuan Jing
- c Department of Preventive Medicine , North Sichuan Medical College , Nanchong , China
| | - Hanmei Xu
- a The Engineering Research Center of Synthetic Polypeptide Drug Discovery and Evaluation of Jiangsu Province , China Pharmaceutical University , Nanjing , China.,d State Key Laboratory of Natural Medicines, Ministry of Education , China Pharmaceutical University , Nanjing , China
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41
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Pereira MT, Malik M, Nostro JA, Mahler GJ, Musselman LP. Effect of dietary additives on intestinal permeability in both Drosophila and a human cell co-culture. Dis Model Mech 2018; 11:dmm034520. [PMID: 30504122 PMCID: PMC6307910 DOI: 10.1242/dmm.034520] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/06/2018] [Indexed: 12/13/2022] Open
Abstract
Increased intestinal barrier permeability has been correlated with aging and disease, including type 2 diabetes, Crohn's disease, celiac disease, multiple sclerosis and irritable bowel syndrome. The prevalence of these ailments has risen together with an increase in industrial food processing and food additive consumption. Additives, including sugar, metal oxide nanoparticles, surfactants and sodium chloride, have all been suggested to increase intestinal permeability. We used two complementary model systems to examine the effects of food additives on gut barrier function: a Drosophila in vivo model and an in vitro human cell co-culture model. Of the additives tested, intestinal permeability was increased most dramatically by high sugar. High sugar also increased feeding but reduced gut and overall animal size. We also examined how food additives affected the activity of a gut mucosal defense factor, intestinal alkaline phosphatase (IAP), which fluctuates with bacterial load and affects intestinal permeability. We found that high sugar reduced IAP activity in both models. Artificial manipulation of the microbiome influenced gut permeability in both models, revealing a complex relationship between the two. This study extends previous work in flies and humans showing that diet can play a role in the health of the gut barrier. Moreover, simple models can be used to study mechanisms underlying the effects of diet on gut permeability and function.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Matthew T Pereira
- Department of Biological Sciences, Binghamton University, Binghamton, New York 13902, USA
| | - Mridu Malik
- Department of Biomedical Engineering, Binghamton University, Binghamton, New York 13902, USA
| | - Jillian A Nostro
- Department of Biological Sciences, Binghamton University, Binghamton, New York 13902, USA
| | - Gretchen J Mahler
- Department of Biomedical Engineering, Binghamton University, Binghamton, New York 13902, USA
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42
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Finkel Y, Stern‐Ginossar N, Schwartz M. Viral Short ORFs and Their Possible Functions. Proteomics 2018; 18:e1700255. [PMID: 29150926 PMCID: PMC7167739 DOI: 10.1002/pmic.201700255] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/06/2017] [Indexed: 12/30/2022]
Abstract
Definition of functional genomic elements is one of the greater challenges of the genomic era. Traditionally, putative short open reading frames (sORFs) coding for less than 100 amino acids were disregarded due to computational and experimental limitations; however, it has become clear over the past several years that translation of sORFs is pervasive and serves diverse functions. The development of ribosome profiling, allowing identification of translated sequences genome wide, revealed wide spread, previously unidentified translation events. New computational methodologies as well as improved mass spectrometry approaches also contributed to the task of annotating translated sORFs in different organisms. Viruses are of special interest due to the selective pressure on their genome size, their rapid and confining evolution, and the potential contribution of novel peptides to the host immune response. Indeed, many functional viral sORFs were characterized to date, and ribosome profiling analyses suggest that this may be the tip of the iceberg. Our computational analyses of sORFs identified by ribosome profiling in DNA viruses demonstrate that they may be enriched in specific features implying that at least some of them are functional. Combination of systematic genome editing strategies with synthetic tagging will take us into the next step-elucidation of the biological relevance and function of this intriguing class of molecules.
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Affiliation(s)
- Yaara Finkel
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | | | - Michal Schwartz
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
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43
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Brunet MA, Levesque SA, Hunting DJ, Cohen AA, Roucou X. Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome Res 2018; 28:609-624. [PMID: 29626081 PMCID: PMC5932603 DOI: 10.1101/gr.230938.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Technological advances promise unprecedented opportunities for whole exome sequencing and proteomic analyses of populations. Currently, data from genome and exome sequencing or proteomic studies are searched against reference genome annotations. This provides the foundation for research and clinical screening for genetic causes of pathologies. However, current genome annotations substantially underestimate the proteomic information encoded within a gene. Numerous studies have now demonstrated the expression and function of alternative (mainly small, sometimes overlapping) ORFs within mature gene transcripts. This has important consequences for the correlation of phenotypes and genotypes. Most alternative ORFs are not yet annotated because of a lack of evidence, and this absence from databases precludes their detection by standard proteomic methods, such as mass spectrometry. Here, we demonstrate how current approaches tend to overlook alternative ORFs, hindering the discovery of new genetic drivers and fundamental research. We discuss available tools and techniques to improve identification of proteins from alternative ORFs and finally suggest a novel annotation system to permit a more complete representation of the transcriptomic and proteomic information contained within a gene. Given the crucial challenge of distinguishing functional ORFs from random ones, the suggested pipeline emphasizes both experimental data and conservation signatures. The addition of alternative ORFs in databases will render identification less serendipitous and advance the pace of research and genomic knowledge. This review highlights the urgent medical and research need to incorporate alternative ORFs in current genome annotations and thus permit their inclusion in hypotheses and models, which relate phenotypes and genotypes.
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Affiliation(s)
- Marie A Brunet
- Biochemistry Department, Université de Sherbrooke, Quebec J1E 4K8, Canada.,Groupe de recherche PRIMUS, Department of Family and Emergency Medicine, Quebec J1H 5N4, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec G1V 0A6, Canada
| | - Sébastien A Levesque
- Pediatric Department, Centre Hospitalier de l'Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Darel J Hunting
- Department of Nuclear Medicine & Radiobiology, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Alan A Cohen
- Groupe de recherche PRIMUS, Department of Family and Emergency Medicine, Quebec J1H 5N4, Canada
| | - Xavier Roucou
- Biochemistry Department, Université de Sherbrooke, Quebec J1E 4K8, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec G1V 0A6, Canada
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44
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The influence of transcript assembly on the proteogenomics discovery of microproteins. PLoS One 2018; 13:e0194518. [PMID: 29584760 PMCID: PMC5870951 DOI: 10.1371/journal.pone.0194518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/05/2018] [Indexed: 11/19/2022] Open
Abstract
Proteogenomics methods have identified many non-annotated protein-coding genes in the human genome. Many of the newly discovered protein-coding genes encode peptides and small proteins, referred to collectively as microproteins. Microproteins are produced through ribosome translation of small open reading frames (smORFs). The discovery of many smORFs reveals a blind spot in traditional gene-finding algorithms for these genes. Biological studies have found roles for microproteins in cell biology and physiology, and the potential that there exists additional bioactive microproteins drives the interest in detection and discovery of these molecules. A key step in any proteogenomics workflow is the assembly of RNA-Seq data into likely mRNA transcripts that are then used to create a searchable protein database. Here we demonstrate that specific features of the assembled transcriptome impact microprotein detection by shotgun proteomics. By tailoring transcript assembly for downstream mass spectrometry searching, we show that we can detect more than double the number of high-quality microprotein candidates and introduce a novel open-source mRNA assembler for proteogenomics (MAPS) that incorporates all of these features. By integrating our specialized assembler, MAPS, and a popular generalized assembler into our proteogenomics pipeline, we detect 45 novel human microproteins from a high quality proteogenomics dataset of a human cell line. We then characterize the features of the novel microproteins, identifying two classes of microproteins. Our work highlights the importance of specialized transcriptome assembly upstream of proteomics validation when searching for short and potentially rare and poorly conserved proteins.
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45
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Translation of neutrally evolving peptides provides a basis for de novo gene evolution. Nat Ecol Evol 2018; 2:890-896. [DOI: 10.1038/s41559-018-0506-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 02/16/2018] [Indexed: 01/29/2023]
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46
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Abstract
Peptides encoded by short open reading frames (sORFs) are usually defined as peptides ≤100 aa long. Usually sORFs were ignored by automatic genome annotation programs due to the high probability of false discovery. However, improved computational tools along with a high-throughput RIBO-seq approach identified a myriad of translated sORFs. Their importance becomes evident as we are gaining experimental validation of their diverse cellular functions. This Review examines various computational and experimental approaches of sORFs identification as well as provides the summary of our current knowledge of their functional roles in cells.
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Affiliation(s)
- Anastasia Chugunova
- Lomonosov Moscow State University , Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology , Skolkovo, Moscow Region 143025, Russia
| | - Tsimafei Navalayeu
- Lomonosov Moscow State University , Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia
| | - Olga Dontsova
- Lomonosov Moscow State University , Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology , Skolkovo, Moscow Region 143025, Russia
| | - Petr Sergiev
- Lomonosov Moscow State University , Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology , Skolkovo, Moscow Region 143025, Russia
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47
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Delcourt V, Staskevicius A, Salzet M, Fournier I, Roucou X. Small Proteins Encoded by Unannotated ORFs are Rising Stars of the Proteome, Confirming Shortcomings in Genome Annotations and Current Vision of an mRNA. Proteomics 2017. [DOI: 10.1002/pmic.201700058] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Vivian Delcourt
- Department of Biochemistry; Université de Sherbrooke; Quebec Canada
- Univ. Lille, INSERM U1192, Laboratoire Protéomique; Réponse Inflammatoire & Spectrométrie de Masse (PRISM); Lille France
- PROTEO, Quebec Network for Research on Protein Function; Structure, and Engineering; Quebec Canada
| | | | - Michel Salzet
- Univ. Lille, INSERM U1192, Laboratoire Protéomique; Réponse Inflammatoire & Spectrométrie de Masse (PRISM); Lille France
| | - Isabelle Fournier
- Univ. Lille, INSERM U1192, Laboratoire Protéomique; Réponse Inflammatoire & Spectrométrie de Masse (PRISM); Lille France
| | - Xavier Roucou
- Department of Biochemistry; Université de Sherbrooke; Quebec Canada
- PROTEO, Quebec Network for Research on Protein Function; Structure, and Engineering; Quebec Canada
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48
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Abstract
A large body of evidence indicates that genome annotation pipelines have biased our view of coding sequences because they generally undersample small proteins and peptides. The recent development of genome-wide translation profiling reveals the prevalence of small/short open reading frames (smORFs or sORFs), which are scattered over all classes of transcripts, including both mRNAs and presumptive long noncoding RNAs. Proteomic approaches further confirm an unexpected variety of smORF-encoded peptides (SEPs), representing an overlooked reservoir of bioactive molecules. Indeed, functional studies in a broad range of species from yeast to humans demonstrate that SEPs can harbor key activities for the control of development, differentiation, and physiology. Here we summarize recent advances in the discovery and functional characterization of smORF/SEPs and discuss why these small players can no longer be ignored with regard to genome function.
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Affiliation(s)
- Serge Plaza
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse, Université Paul Sabatier, 31326 Castanet Tolosan, France; .,CNRS, UMR5546, Laboratoire de Recherches en Sciences Végétales, 31326 Castanet Tolosan, France
| | - Gerben Menschaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, University of Ghent, 9000 Gent, Belgium
| | - François Payre
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier, 31062 Toulouse, France;
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49
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50
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Functions of long non-coding RNAs in human disease and their conservation in Drosophila development. Biochem Soc Trans 2017; 45:895-904. [PMID: 28673935 DOI: 10.1042/bst20160428] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/18/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]
Abstract
Genomic analysis has found that the transcriptome in both humans and Drosophila melanogaster features large numbers of long non-coding RNA transcripts (lncRNAs). This recently discovered class of RNAs regulates gene expression in diverse ways and has been involved in a large variety of important biological functions. Importantly, an increasing number of lncRNAs have also been associated with a range of human diseases, including cancer. Comparative analyses of their functions among these organisms suggest that some of their modes of action appear to be conserved. This highlights the importance of model organisms such as Drosophila, which shares many gene regulatory networks with humans, in understanding lncRNA function and its possible impact in human health. This review discusses some known functions and mechanisms of action of lncRNAs and their implication in human diseases, together with their functional conservation and relevance in Drosophila development.
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