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Schultz PG. Synthesis at the Interface of Chemistry and Biology. Acc Chem Res 2024; 57:2631-2642. [PMID: 39198974 DOI: 10.1021/acs.accounts.4c00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2024]
Abstract
ConspectusChemical synthesis as a tool to control the structure and properties of matter is at the heart of chemistry─from the synthesis of fine chemicals and polymers to drugs and solid-state materials. But as the field evolves to tackle larger and larger molecules and molecular complexes, the traditional tools of synthetic chemistry become limiting. In contrast, Mother Nature has developed very different strategies to create the macromolecules and molecular systems that make up the living cell. Our focus has been to ask whether we can use the synthetic strategies and machinery of Mother Nature, together with modern chemical tools, to create new macromolecules, and even whole organisms with properties not existing in nature. One such example involves reprogramming the complex, multicomponent machinery of ribosomal protein synthesis to add new building blocks to the genetic code, overcoming a billion-year constraint on the chemical nature of proteins. This methodology exploits the concept of bioorthogonality to add unique codons, tRNAs and aminoacyl-tRNA synthetases to cells to encode amino acids with physical, chemical and biological properties not found in nature. As a result, we can make precise changes to the structures of proteins, much like those made by chemists to small molecules and beyond those possible by biological approaches alone. This technology has made it possible to probe protein structure and function in vitro and in vivo in ways heretofore not possible, and to make therapeutic proteins with enhanced pharmacology. A second example involves exploiting the molecular diversity of the humoral immune system together with synthetic transition state analogues to make catalytic antibodies, and then expanding this diversity-based strategy (new to chemists at the time) to drug discovery and materials science. This work ushered in a new nature-inspired synthetic strategy in which large libraries of natural or synthetic molecules are designed and then rationally selected or screened for new function, increasing the efficiency by which we can explore chemical space for new physical, chemical and biological properties. A final example is the use of large chemical libraries, robotics and high throughput phenotypic cellular screens to identify small synthetic molecules that can be used to probe and manipulate the complex biology of the cell, exemplified by druglike molecules that control cell fate. This approach provides new insights into complex biology that complements genomic approaches and can lead to new drugs that act by novel mechanisms of action, for example to selectively regenerate tissues. These and other advances have been made possible by using our knowledge of molecular structure and reactivity hand in hand with our understanding of and ability to manipulate the complex machinery of living cells, opening a new frontier in synthesis. This Account overviews the work in my lab and with our collaborators, from our early days to the present, that revolves around this central theme.
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Affiliation(s)
- Peter G Schultz
- Department of Chemistry, L.S. Sam Skaggs Presidential Chair, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024. [PMID: 39235427 DOI: 10.1021/acs.chemrev.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
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Affiliation(s)
- Daniel L Dunkelmann
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
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Szafron LA, Iwanicka-Nowicka R, Podgorska A, Bonna AM, Sobiczewski P, Kupryjanczyk J, Szafron LM. The Clinical Significance of CRNDE Gene Methylation, Polymorphisms, and CRNDEP Micropeptide Expression in Ovarian Tumors. Int J Mol Sci 2024; 25:7531. [PMID: 39062774 PMCID: PMC11277161 DOI: 10.3390/ijms25147531] [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: 04/28/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
CRNDE is an oncogene expressed as a long non-coding RNA. However, our team previously reported that the CRNDE gene also encodes a micropeptide, CRNDEP. The amino acid sequence of CRNDEP has recently been revealed by other researchers, too. This study aimed to investigate genetic alterations within the CRNDEP-coding region of the CRNDE gene, methylation profiling of this gene, and CRNDEP expression analysis. All investigations were performed on clinical material from patients with ovarian tumors of diverse aggressiveness. We found that CRNDEP levels were significantly elevated in highly aggressive tumors compared to benign neoplasms. Consistently, a high level of this micropeptide was a negative, independent, prognostic, and predictive factor in high-grade ovarian cancer (hgOvCa) patients. The cancer-promoting role of CRNDE(P), shown in our recent study, was also supported by genetic and epigenetic results obtained herein, revealing no CRNDEP-disrupting mutations in any clinical sample. Moreover, in borderline ovarian tumors (BOTS), but not in ovarian cancers, the presence of a single nucleotide polymorphism in CRNDE, rs115515594, significantly increased the risk of recurrence. Consistently, in BOTS only, the same genetic variant was highly overrepresented compared to healthy individuals. We also discovered that hypomethylation of CRNDE is associated with increased aggressiveness of ovarian tumors. Accordingly, hypomethylation of this gene's promoter/first exon correlated with hgOvCa resistance to chemotherapy, but only in specimens with accumulation of the TP53 tumor suppressor protein. Taken together, these results contribute to a better understanding of the role of CRNDE(P) in tumorigenesis and potentially may lead to improvements in screening, diagnosis, and treatment of ovarian neoplasms.
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Affiliation(s)
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Agnieszka Podgorska
- Cancer Molecular and Genetic Diagnostics Department, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | | | - Piotr Sobiczewski
- Department of Gynecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jolanta Kupryjanczyk
- Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland;
| | - Lukasz Michal Szafron
- Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
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de Souza EV, Bizarro CV. Identification of Novel Bacterial Microproteins Encoded by Small Open Reading Frames Using a Computational Proteogenomics Workflow. Methods Mol Biol 2024; 2836:19-34. [PMID: 38995533 DOI: 10.1007/978-1-0716-4007-4_2] [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] [Indexed: 07/13/2024]
Abstract
Genome annotation has historically ignored small open reading frames (smORFs), which encode a class of proteins shorter than 100 amino acids, collectively referred to as microproteins. This cutoff was established to avoid thousands of false positives due to limitations of pure genomics pipelines. Proteogenomics, a computational approach that combines genomics, transcriptomics, and proteomics, makes it possible to accurately identify these short sequences by overlaying different levels of omics evidence. In this chapter, we showcase the use of μProteInS, a bioinformatics pipeline developed for the identification of unannotated microproteins encoded by smORFs in bacteria. The workflow covers all the steps from quality control and transcriptome assembly to the scoring and post-processing of mass spectrometry data. Additionally, we provide an example on how to apply the pipeline's machine learning method to identify high-confidence spectra and pinpoint the most reliable identifications from large datasets.
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Affiliation(s)
- Eduardo Vieira de Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristiano Valim Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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5
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Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Zhang Z, Liu W, Lee HRL, Tang X, He W, Islam N, Jain A, Chiu Y, Cao S, Diao Y, Meyer-Gauen S, Höök M, Malovannaya A, Li W, Hu M, Wang W, Xu H, Kopetz S, Chen Y. CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nat Struct Mol Biol 2023; 30:1878-1892. [PMID: 37932451 PMCID: PMC10716047 DOI: 10.1038/s41594-023-01117-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 09/06/2023] [Indexed: 11/08/2023]
Abstract
Emerging evidence suggests that cryptic translation beyond the annotated translatome produces proteins with developmental or physiological functions. However, functions of cryptic non-canonical open reading frames (ORFs) in cancer remain largely unknown. To fill this gap and systematically identify colorectal cancer (CRC) dependency on non-canonical ORFs, we apply an integrative multiomic strategy, combining ribosome profiling and a CRISPR-Cas9 knockout screen with large-scale analysis of molecular and clinical data. Many such ORFs are upregulated in CRC compared to normal tissues and are associated with clinically relevant molecular subtypes. We confirm the in vivo tumor-promoting function of the microprotein SMIMP, encoded by a primate-specific, long noncoding RNA, the expression of which is associated with poor prognosis in CRC, is low in normal tissues and is specifically elevated in CRC and several other cancer types. Mechanistically, SMIMP interacts with the ATPase-forming domains of SMC1A, the core subunit of the cohesin complex, and facilitates SMC1A binding to cis-regulatory elements to promote epigenetic repression of the tumor-suppressive cell cycle regulators encoded by CDKN1A and CDKN2B. Thus, our study reveals a cryptic microprotein as an important component of cohesin-mediated gene regulation and suggests that the 'dark' proteome, encoded by cryptic non-canonical ORFs, may contain potential therapeutic or diagnostic targets.
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Affiliation(s)
- Caishang Zheng
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kangyu Lin
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dandan He
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Sema4, Inc., Stamford, CT, USA
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ganiraju Manyam
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Texas A&M Health Science Center, Institute of Biosciences of Technology, Houston, TX, USA
| | - Hye Rin Lindsay Lee
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nelufa Islam
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA
| | - Antrix Jain
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaolong Cao
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Department of Orthopedic Surgery, Duke University Medical Center, Durham, NC, USA
| | - Sherita Meyer-Gauen
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Magnus Höök
- Center for Infectious and Inflammatory Diseases, Texas A&M Health Science Center, Institute of Biosciences of Technology, Houston, TX, USA
| | - Anna Malovannaya
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Han Xu
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Genetics and Epigenetics Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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Xie L, Bowman ME, Louie GV, Zhang C, Ardejani MS, Huang X, Chu Q, Donaldson CJ, Vaughan JM, Shan H, Powers ET, Kelly JW, Lyumkis D, Noel JP, Saghatelian A. Biochemistry and Protein Interactions of the CYREN Microprotein. Biochemistry 2023; 62:3050-3060. [PMID: 37813856 DOI: 10.1021/acs.biochem.3c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Over the past decade, advances in genomics have identified thousands of additional protein-coding small open reading frames (smORFs) missed by traditional gene finding approaches. These smORFs encode peptides and small proteins, commonly termed micropeptides or microproteins. Several of these newly discovered microproteins have biological functions and operate through interactions with proteins and protein complexes within the cell. CYREN1 is a characterized microprotein that regulates double-strand break repair in mammalian cells through interaction with Ku70/80 heterodimer. Ku70/80 binds to and stabilizes double-strand breaks and recruits the machinery needed for nonhomologous end join repair. In this study, we examined the biochemical properties of CYREN1 to better understand and explain its cellular protein interactions. Our findings support that CYREN1 is an intrinsically disordered microprotein and this disordered structure allows it to enriches several proteins, including a newly discovered interaction with SF3B1 via a distinct short linear motif (SLiMs) on CYREN1. Since many microproteins are predicted to be disordered, CYREN1 is an exemplar of how microproteins interact with other proteins and reveals an unknown scaffolding function of this microprotein that may link NHEJ and splicing.
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Affiliation(s)
- Lina Xie
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gordon V Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Cheng Zhang
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maziar S Ardejani
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xuemei Huang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
| | - Qian Chu
- Department of Pharmacy, China Pharmaceutical University, Nanjing 210009, Jiangsu, China
| | - Cynthia J Donaldson
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joan M Vaughan
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Huanqi Shan
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Evan T Powers
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dimitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Saghatelian
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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Sherlock ME, Baquero Galvis L, Vicens Q, Kieft JS, Jagannathan S. Principles, mechanisms, and biological implications of translation termination-reinitiation. RNA (NEW YORK, N.Y.) 2023; 29:865-884. [PMID: 37024263 PMCID: PMC10275272 DOI: 10.1261/rna.079375.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/28/2023] [Indexed: 06/11/2023]
Abstract
The gene expression pathway from DNA sequence to functional protein is not as straightforward as simple depictions of the central dogma might suggest. Each step is highly regulated, with complex and only partially understood molecular mechanisms at play. Translation is one step where the "one gene-one protein" paradigm breaks down, as often a single mature eukaryotic mRNA leads to more than one protein product. One way this occurs is through translation reinitiation, in which a ribosome starts making protein from one initiation site, translates until it terminates at a stop codon, but then escapes normal recycling steps and subsequently reinitiates at a different downstream site. This process is now recognized as both important and widespread, but we are only beginning to understand the interplay of factors involved in termination, recycling, and initiation that cause reinitiation events. There appear to be several ways to subvert recycling to achieve productive reinitiation, different types of stresses or signals that trigger this process, and the mechanism may depend in part on where the event occurs in the body of an mRNA. This perspective reviews the unique characteristics and mechanisms of reinitiation events, highlights the similarities and differences between three major scenarios of reinitiation, and raises outstanding questions that are promising avenues for future research.
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Affiliation(s)
- Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Laura Baquero Galvis
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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Chen Y, Cao X, Loh KH, Slavoff SA. Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides. Biochem Soc Trans 2023; 51:1071-1082. [PMID: 37171061 PMCID: PMC10317152 DOI: 10.1042/bst20221074] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023]
Abstract
Thousands of unannotated small and alternative open reading frames (smORFs and alt-ORFs, respectively) have recently been revealed in mammalian genomes. While hundreds of mammalian smORF- and alt-ORF-encoded proteins (SEPs and alt-proteins, respectively) affect cell proliferation, the overwhelming majority of smORFs and alt-ORFs remain uncharacterized at the molecular level. Complicating the task of identifying the biological roles of smORFs and alt-ORFs, the SEPs and alt-proteins that they encode exhibit limited sequence homology to protein domains of known function. Experimental techniques for the functionalization of these gene classes are therefore required. Approaches combining chemical labeling and quantitative proteomics have greatly advanced our ability to identify and characterize functional SEPs and alt-proteins in high throughput. In this review, we briefly describe the principles of proteomic discovery of SEPs and alt-proteins, then summarize how these technologies interface with chemical labeling for identification of SEPs and alt-proteins with specific properties, as well as in defining the interactome of SEPs and alt-proteins.
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Affiliation(s)
- Yanran Chen
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, U.S.A
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ken H. Loh
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, U.S.A
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, U.S.A
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9
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Kozuka-Hata H, Hiroki T, Miyamura N, Kitamura A, Tsumoto K, Inoue JI, Oyama M. Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of Non-Canonical Short Open Reading Frames. Biomolecules 2023; 13:979. [PMID: 37371559 DOI: 10.3390/biom13060979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Abnormal expression of histone deacetylases (HDACs) is reported to be associated with angiogenesis, metastasis and chemotherapy resistance regarding cancer in a wide range of previous studies. Suberoylanilide hydroxamic acid (SAHA) is well known to function as a pan-inhibitor for HDACs and recognized as one of the therapeutic drug candidates to epigenetically coordinate cancer cell fate regulation on a genomic scale. Here, we established a Real-Time Search (RTS)-assisted mass spectrometric platform for system-wide quantification of translated products encoded by non-canonical short open reading frames (ORFs) as well as already annotated protein coding sequences (CDSs) on the human transciptome and applied this methodology to quantitative proteomic analyses of suberoylanilide hydroxamic acid (SAHA)-treated human HeLa cells to evaluate proteome-wide regulation in response to drug perturbation. Very intriguingly, our RTS-based in-depth proteomic analysis enabled us to identify approximately 5000 novel peptides from the ribosome profiling-based short ORFs encoded in the diversified regions on presumed 'non-coding' nucleotide sequences of mRNAs as well as lncRNAs and nonsense mediated decay (NMD) transcripts. Furthermore, TMT-based multiplex large-scale quantification of the whole proteome changes upon differential SAHA treatment unveiled dose-dependent selective translational regulation of a limited fraction of the non-canonical short ORFs in addition to key cell cycle/proliferation-related molecules such as UBE2C, CENPF and PRC1. Our study provided the first system-wide landscape of drug-perturbed translational modulation on both canonical and non-canonical proteome dynamics in human cancer cells.
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Affiliation(s)
- Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Tomoko Hiroki
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Naoaki Miyamura
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Aya Kitamura
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jun-Ichiro Inoue
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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10
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Chothani S, Ho L, Schafer S, Rackham O. Discovering microproteins: making the most of ribosome profiling data. RNA Biol 2023; 20:943-954. [PMID: 38013207 PMCID: PMC10730196 DOI: 10.1080/15476286.2023.2279845] [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] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
Building a reference set of protein-coding open reading frames (ORFs) has revolutionized biological process discovery and understanding. Traditionally, gene models have been confirmed using cDNA sequencing and encoded translated regions inferred using sequence-based detection of start and stop combinations longer than 100 amino-acids to prevent false positives. This has led to small ORFs (smORFs) and their encoded proteins left un-annotated. Ribo-seq allows deciphering translated regions from untranslated irrespective of the length. In this review, we describe the power of Ribo-seq data in detection of smORFs while discussing the major challenge posed by data-quality, -depth and -sparseness in identifying the start and end of smORF translation. In particular, we outline smORF cataloguing efforts in humans and the large differences that have arisen due to variation in data, methods and assumptions. Although current versions of smORF reference sets can already be used as a powerful tool for hypothesis generation, we recommend that future editions should consider these data limitations and adopt unified processing for the community to establish a canonical catalogue of translated smORFs.
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Affiliation(s)
- Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Owen Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
- School of Biological Sciences, University of Southampton, Southampton, UK
- The Alan Turing Institute, The British Library, London, UK
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11
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Treichel AJ, Bazzini AA. Casting CRISPR-Cas13d to fish for microprotein functions in animal development. iScience 2022; 25:105547. [PMID: 36444300 PMCID: PMC9700322 DOI: 10.1016/j.isci.2022.105547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Protein coding genes were originally identified with sequence-based definitions that included a 100-codon cutoff to avoid annotating irrelevant open reading frames. However, many active proteins contain less than 100 amino acids. Indeed, functional genetics, ribosome profiling, and proteomic profiling have identified many short, translated open reading frames, including those with biologically active peptide products (microproteins). Yet, functions for most of these peptide products remain unknown. Because microproteins often act as key signals or fine-tune processes, animal development has already revealed functions for a handful of microproteins and provides an ideal context to uncover additional microprotein functions. However, many mRNAs during early development are maternally provided and hinder targeted mutagenesis approaches to characterize developmental microprotein functions. The recently established, RNA-targeting CRISPR-Cas13d system in zebrafish overcomes this barrier and produces potent knockdown of targeted mRNA, including maternally provided mRNA, and enables flexible, efficient interrogation of microprotein functions in animal development.
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Affiliation(s)
| | - Ariel Alejandro Bazzini
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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12
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Yang Y, Wang H, Zhang Y, Chen L, Chen G, Bao Z, Yang Y, Xie Z, Zhao Q. An Optimized Proteomics Approach Reveals Novel Alternative Proteins in Mouse Liver Development. Mol Cell Proteomics 2022; 22:100480. [PMID: 36494044 PMCID: PMC9823216 DOI: 10.1016/j.mcpro.2022.100480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/15/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
Alternative ORFs (AltORFs) are unannotated sequences in genome that encode novel peptides or proteins named alternative proteins (AltProts). Although ribosome profiling and bioinformatics predict a large number of AltProts, mass spectrometry as the only direct way of identification is hampered by the short lengths and relative low abundance of AltProts. There is an urgent need for improvement of mass spectrometry methodologies for AltProt identification. Here, we report an approach based on size-exclusion chromatography for simultaneous enrichment and fractionation of AltProts from complex proteome. This method greatly simplifies the variance of AltProts discovery by enriching small proteins smaller than 40 kDa. In a systematic comparison between 10 methods, the approach we reported enabled the discovery of more AltProts with overall higher intensities, with less cost of time and effort compared to other workflows. We applied this approach to identify 89 novel AltProts from mouse liver, 39 of which were differentially expressed between embryonic and adult mice. During embryonic development, the upregulated AltProts were mainly involved in biological pathways on RNA splicing and processing, whereas the AltProts involved in metabolisms were more active in adult livers. Our study not only provides an effective approach for identifying AltProts but also novel AltProts that are potentially important in developmental biology.
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Affiliation(s)
- Ying Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yuanliang Zhang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Lei Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Gennong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical School, Beijing, China
| | - Yang Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR, China,For correspondence: Qian Zhao
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13
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Zannella C, Chianese A, Greco G, Santella B, Squillaci G, Monti A, Doti N, Sanna G, Manzin A, Morana A, De Filippis A, D’Angelo G, Palmieri F, Franci G, Galdiero M. Design of Three Residues Peptides against SARS-CoV-2 Infection. Viruses 2022; 14:v14102103. [PMID: 36298659 PMCID: PMC9612326 DOI: 10.3390/v14102103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/11/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022] Open
Abstract
The continuous and rapid spread of the COVID-19 pandemic has emphasized the need to seek new therapeutic and prophylactic treatments. Peptide inhibitors are a valid alternative approach for the treatment of emerging viral infections, mainly due to their low toxicity and high efficiency. Recently, two small nucleotide signatures were identified in the genome of some members of the Coronaviridae family and many other human pathogens. In this study, we investigated whether the corresponding amino acid sequences of such nucleotide sequences could have effects on the viral infection of two representative human coronaviruses: HCoV-OC43 and SARS-CoV-2. Our results showed that the synthetic peptides analyzed inhibit the infection of both coronaviruses in a dose-dependent manner by binding the RBD of the Spike protein, as suggested by molecular docking and validated by biochemical studies. The peptides tested do not provide toxicity on cultured cells or human erythrocytes and are resistant to human serum proteases, indicating that they may be very promising antiviral peptides.
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Affiliation(s)
- Carla Zannella
- Department of Experimental Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Annalisa Chianese
- Department of Experimental Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Giuseppe Greco
- Department of Experimental Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Biagio Santella
- Department of Experimental Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Giuseppe Squillaci
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80134 Naples, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80134 Naples, Italy
| | - Giuseppina Sanna
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, 09042 Cagliari, Italy
| | - Aldo Manzin
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, 09042 Cagliari, Italy
| | - Alessandra Morana
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Anna De Filippis
- Department of Experimental Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Gianni D’Angelo
- Department of Computer Science, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Francesco Palmieri
- Department of Computer Science, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy
- Correspondence:
| | - Massimiliano Galdiero
- Department of Experimental Medicine, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy
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14
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Malekos E, Carpenter S. Short open reading frame genes in innate immunity: from discovery to characterization. Trends Immunol 2022; 43:741-756. [PMID: 35965152 PMCID: PMC10118063 DOI: 10.1016/j.it.2022.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/27/2022]
Abstract
Next-generation sequencing (NGS) technologies have greatly expanded the size of the known transcriptome. Many newly discovered transcripts are classified as long noncoding RNAs (lncRNAs) which are assumed to affect phenotype through sequence and structure and not via translated protein products despite the vast majority of them harboring short open reading frames (sORFs). Recent advances have demonstrated that the noncoding designation is incorrect in many cases and that sORF-encoded peptides (SEPs) translated from these transcripts are important contributors to diverse biological processes. Interest in SEPs is at an early stage and there is evidence for the existence of thousands of SEPs that are yet unstudied. We hope to pique interest in investigating this unexplored proteome by providing a discussion of SEP characterization generally and describing specific discoveries in innate immunity.
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Affiliation(s)
- Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Susan Carpenter
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA; Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
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15
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Chothani SP, Adami E, Widjaja AA, Langley SR, Viswanathan S, Pua CJ, Zhihao NT, Harmston N, D'Agostino G, Whiffin N, Mao W, Ouyang JF, Lim WW, Lim S, Lee CQE, Grubman A, Chen J, Kovalik JP, Tryggvason K, Polo JM, Ho L, Cook SA, Rackham OJL, Schafer S. A high-resolution map of human RNA translation. Mol Cell 2022; 82:2885-2899.e8. [PMID: 35841888 DOI: 10.1016/j.molcel.2022.06.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 03/10/2022] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome.
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Affiliation(s)
- Sonia P Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anissa A Widjaja
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Chee Jian Pua
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Nevin Tham Zhihao
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Science Division, Yale-NUS College, Singapore 138527, Singapore
| | - Giuseppe D'Agostino
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nicola Whiffin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Wang Mao
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Wei Wen Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Shiqi Lim
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Cheryl Q E Lee
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - J P Kovalik
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore; London Institute of Medical Sciences, London W12 ONN, UK
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; School of Biological Sciences, University of Southampton, Southampton, UK.
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore.
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16
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Na Z, Dai X, Zheng SJ, Bryant CJ, Loh KH, Su H, Luo Y, Buhagiar AF, Cao X, Baserga SJ, Chen S, Slavoff SA. Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID. Mol Cell 2022; 82:2900-2911.e7. [PMID: 35905735 PMCID: PMC9662605 DOI: 10.1016/j.molcel.2022.06.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/08/2022] [Accepted: 06/29/2022] [Indexed: 11/15/2022]
Abstract
Proteogenomic identification of translated small open reading frames has revealed thousands of previously unannotated, largely uncharacterized microproteins, or polypeptides of less than 100 amino acids, and alternative proteins (alt-proteins) that are co-encoded with canonical proteins and are often larger. The subcellular localizations of microproteins and alt-proteins are generally unknown but can have significant implications for their functions. Proximity biotinylation is an attractive approach to define the protein composition of subcellular compartments in cells and in animals. Here, we developed a high-throughput technology to map unannotated microproteins and alt-proteins to subcellular localizations by proximity biotinylation with TurboID (MicroID). More than 150 microproteins and alt-proteins are associated with subnuclear organelles. One alt-protein, alt-LAMA3, localizes to the nucleolus and functions in pre-rRNA transcription. We applied MicroID in a mouse model, validating expression of a conserved nuclear microprotein, and establishing MicroID for discovery of microproteins and alt-proteins in vivo.
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Affiliation(s)
- Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Xiaoyun Dai
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Shu-Jian Zheng
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Ken H Loh
- Laboratory of Molecular Genetics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Haomiao Su
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Yang Luo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Amber F Buhagiar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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17
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Gu H, Song J, Chen Y, Wang Y, Tan X, Zhao H. Inflammation-Related LncRNAs Signature for Prognosis and Immune Response Evaluation in Uterine Corpus Endometrial Carcinoma. Front Oncol 2022; 12:923641. [PMID: 35719911 PMCID: PMC9201290 DOI: 10.3389/fonc.2022.923641] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Backgrounds Uterine corpus endometrial carcinoma (UCEC) is one of the greatest threats on the female reproductive system. The aim of this study is to explore the inflammation-related LncRNA (IRLs) signature predicting the clinical outcomes and response of UCEC patients to immunotherapy and chemotherapy. Methods Consensus clustering analysis was employed to determine inflammation-related subtype. Cox regression methods were used to unearth potential prognostic IRLs and set up a risk model. The prognostic value of the prognostic model was calculated by the Kaplan-Meier method, receiver operating characteristic (ROC) curves, and univariate and multivariate analyses. Differential abundance of immune cell infiltration, expression levels of immunomodulators, the status of tumor mutation burden (TMB), the response to immune checkpoint inhibitors (ICIs), drug sensitivity, and functional enrichment in different risk groups were also explored. Finally, we used quantitative real-time PCR (qRT-PCR) to confirm the expression patterns of model IRLs in clinical specimens. Results All UCEC cases were divided into two clusters (C1 = 454) and (C2 = 57) which had significant differences in prognosis and immune status. Five hub IRLs were selected to develop an IRL prognostic signature (IRLPS) which had value in forecasting the clinical outcome of UCEC patients. Biological processes related to tumor and immune response were screened. Function enrichment algorithm showed tumor signaling pathways (ERBB signaling, TGF-β signaling, and Wnt signaling) were remarkably activated in high-risk group scores. In addition, the high-risk group had a higher infiltration level of M2 macrophages and lower TMB value, suggesting patients with high risk were prone to a immunosuppressive status. Furthermore, we determined several potential molecular drugs for UCEC. Conclusion We successfully identified a novel molecular subtype and inflammation-related prognostic model for UCEC. Our constructed risk signature can be employed to assess the survival of UCEC patients and offer a valuable reference for clinical treatment regimens.
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Affiliation(s)
- Hongmei Gu
- Department of Radiotherapy Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiahang Song
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yizhang Chen
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yichun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaofang Tan
- Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, China
| | - Hongyu Zhao
- Department of Radiotherapy Oncology, Affiliated Hospital of Nantong University, Nantong, China
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18
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Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency. PLoS Genet 2022; 18:e1010267. [PMID: 35714159 PMCID: PMC9246224 DOI: 10.1371/journal.pgen.1010267] [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: 01/25/2022] [Revised: 06/30/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
The conserved nucleic acid binding protein Translin contributes to numerous facets of mammalian biology and genetic diseases. It was first identified as a binder of cancer-associated chromosomal translocation breakpoint junctions leading to the suggestion that it was involved in genetic recombination. With a paralogous partner protein, Trax, Translin has subsequently been found to form a hetero-octomeric RNase complex that drives some of its functions, including passenger strand removal in RNA interference (RNAi). The Translin-Trax complex also degrades the precursors to tumour suppressing microRNAs in cancers deficient for the RNase III Dicer. This oncogenic activity has resulted in the Translin-Trax complex being explored as a therapeutic target. Additionally, Translin and Trax have been implicated in a wider range of biological functions ranging from sleep regulation to telomere transcript control. Here we reveal a Trax- and RNAi-independent function for Translin in dissociating RNA polymerase II from its genomic template, with loss of Translin function resulting in increased transcription-associated recombination and elevated genome instability. This provides genetic insight into the longstanding question of how Translin might influence chromosomal rearrangements in human genetic diseases and provides important functional understanding of an oncological therapeutic target. Human genetic diseases, including cancers, are frequently driven by substantial changes to chromosomes, including translocations, where one arm of a chromosome is exchanged for another. The human nucleic acid binding protein Translin was first identified by its ability to bind to the chromosomal sites at which some of these translocations occur. This resulted in Translin being implicated in the mechanism that generated the translocation and thus the associated disease state. However, since its discovery there has been little evidence to directly indicate Translin does contribute to this process. It is, however, known to contribute to a number of biological functions including, amongst others, neurological regulation, sleep control, vascular stiffening, cancer immunomodulation and it has been recently identified as a potential therapeutic target in some cancers. Here we demonstrate that Translin has conserved function in genome stability maintenance when other primary pathways are defective, a function independent of a key binding partner protein, Trax. Specifically, we demonstrate that Translin contributes to minimizing the deleterious genome destabilizing effects of retaining gene expression machineries on chromosomes. This offers the first evidence for how Translin might contribute to genetic disease-causing chromosomal changes and offers insight to inform therapeutic design.
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19
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Abstract
The mechanisms that explain mitochondrial dysfunction in aging and healthspan continue to be studied, but one element has been unexplored: microproteins. Small open reading frames in circular mitochondria DNA can encode multiple microproteins, called mitochondria-derived peptides (MDPs). Currently, eight MDPs have been published: humanin, MOTS-c, and SHLPs 1–6. This Review describes recent advances in microprotein discovery with a focus on MDPs. It discusses what is currently known about MDPs in aging and how this new understanding could add to the way we understand age-related diseases including type 2 diabetes, cancer, and neurodegenerative diseases at the genomic, proteomic, and drug-development levels.
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20
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Veale CGL, Talukdar A, Vauzeilles B. ICBS 2021: Looking Toward the Next Decade of Chemical Biology. ACS Chem Biol 2022; 17:728-743. [PMID: 35293726 DOI: 10.1021/acschembio.2c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton G. L. Veale
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Boris Vauzeilles
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
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21
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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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22
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The dark proteome: translation from noncanonical open reading frames. Trends Cell Biol 2022; 32:243-258. [PMID: 34844857 PMCID: PMC8934435 DOI: 10.1016/j.tcb.2021.10.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023]
Abstract
Omics-based technologies have revolutionized our understanding of the coding potential of the genome. In particular, these studies revealed widespread unannotated open reading frames (ORFs) throughout genomes and that these regions have the potential to encode novel functional (micro-)proteins and/or hold regulatory roles. However, despite their genomic prevalence, relatively few of these noncanonical ORFs have been functionally characterized, likely in part due to their under-recognition by the broader scientific community. The few that have been investigated in detail have demonstrated their essentiality in critical and divergent biological processes. As such, here we aim to discuss recent advances in understanding the diversity of noncanonical ORFs and their roles, as well as detail biologically important examples within the context of the mammalian genome.
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23
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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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24
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Kute PM, Soukarieh O, Tjeldnes H, Trégouët DA, Valen E. Small Open Reading Frames, How to Find Them and Determine Their Function. Front Genet 2022; 12:796060. [PMID: 35154250 PMCID: PMC8831751 DOI: 10.3389/fgene.2021.796060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022] Open
Abstract
Advances in genomics and molecular biology have revealed an abundance of small open reading frames (sORFs) across all types of transcripts. While these sORFs are often assumed to be non-functional, many have been implicated in physiological functions and a significant number of sORFs have been described in human diseases. Thus, sORFs may represent a hidden repository of functional elements that could serve as therapeutic targets. Unlike protein-coding genes, it is not necessarily the encoded peptide of an sORF that enacts its function, sometimes simply the act of translating an sORF might have a regulatory role. Indeed, the most studied sORFs are located in the 5′UTRs of coding transcripts and can have a regulatory impact on the translation of the downstream protein-coding sequence. However, sORFs have also been abundantly identified in non-coding RNAs including lncRNAs, circular RNAs and ribosomal RNAs suggesting that sORFs may be diverse in function. Of the many different experimental methods used to discover sORFs, the most commonly used are ribosome profiling and mass spectrometry. These can confirm interactions between transcripts and ribosomes and the production of a peptide, respectively. Extensions to ribosome profiling, which also capture scanning ribosomes, have further made it possible to see how sORFs impact the translation initiation of mRNAs. While high-throughput techniques have made the identification of sORFs less difficult, defining their function, if any, is typically more challenging. Together, the abundance and potential function of many of these sORFs argues for the necessity of including sORFs in gene annotations and systematically characterizing these to understand their potential functional roles. In this review, we will focus on the high-throughput methods used in the detection and characterization of sORFs and discuss techniques for validation and functional characterization.
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Affiliation(s)
- Preeti Madhav Kute
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Omar Soukarieh
- Department of Molecular Epidemiology Of Vascular and Brain Disorders, INSERM, BPH, U1219, University of Bordeaux, Bordeaux, France
| | - Håkon Tjeldnes
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - David-Alexandre Trégouët
- Department of Molecular Epidemiology Of Vascular and Brain Disorders, INSERM, BPH, U1219, University of Bordeaux, Bordeaux, France
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- *Correspondence: Eivind Valen,
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25
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Ahrens CH, Wade JT, Champion MM, Langer JD. A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry. J Bacteriol 2022; 204:e0035321. [PMID: 34748388 PMCID: PMC8765459 DOI: 10.1128/jb.00353-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.
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Affiliation(s)
- Christian H. Ahrens
- Agroscope, Method Development and Analytics & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Julian D. Langer
- Mass Spectrometry and Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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26
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OUP accepted manuscript. Bioinformatics 2022; 38:2612-2614. [DOI: 10.1093/bioinformatics/btac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
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27
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Chen L, Yang Y, Zhang Y, Li K, Cai H, Wang H, Zhao Q. The Small Open Reading Frame-Encoded Peptides: Advances in Methodologies and Functional Studies. Chembiochem 2021; 23:e202100534. [PMID: 34862721 DOI: 10.1002/cbic.202100534] [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: 10/06/2021] [Revised: 11/15/2021] [Indexed: 11/07/2022]
Abstract
Small open reading frames (sORFs) are an important class of genes with less than 100 codons. They were historically annotated as noncoding or even junk sequences. In recent years, accumulating evidence suggests that sORFs could encode a considerable number of polypeptides, many of which play important roles in both physiology and disease pathology. However, it has been technically challenging to directly detect sORF-encoded peptides (SEPs). Here, we discuss the latest advances in methodologies for identifying SEPs with mass spectrometry, as well as the progress on functional studies of SEPs.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, 999077, P. R. China.,Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, 999077, P. R. China
| | - Ying Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, 999077, P. R. China
| | - Yuanliang Zhang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, 999077, P. R. China
| | - Kecheng Li
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, 999077, P. R. China
| | - Hongmin Cai
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510623, P. R. China
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510623, P. R. China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, 999077, P. R. China
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28
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Abstract
The maturation of chemical synthesis during the 20th century has elevated the discipline from a largely empirical into a rational science. This ability to purposefully craft matter at the molecular level has put chemists in a privileged position to contribute to progress in neighboring natural sciences. Recently, we have witnessed another major advance in the field in which chemists use chemical and biological "synthetic" methods together to alter the structures and properties of biological macromolecules in ways heretofore unimagined. This interdisciplinary approach to synthesis has even allowed us to expand upon the defining characteristics of living organisms at the molecular level. In this perspective, we present a case study for the successful addition of new chemistries to the fundamental processes of the central dogma of molecular biology, exemplified by the expansion of the genetic code.
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Affiliation(s)
- Christian S. Diercks
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - David A. Dik
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- These authors contributed equally
| | - Peter G. Schultz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Lead contact
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29
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Chen L, Zhang Y, Yang Y, Yang Y, Li H, Dong X, Wang H, Xie Z, Zhao Q. An Integrated Approach for Discovering Noncanonical MHC-I Peptides Encoded by Small Open Reading Frames. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2346-2357. [PMID: 34260243 DOI: 10.1021/jasms.1c00076] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
MHC-I peptides are a group of important immunopeptides presented by major histocompatibility complex (MHC) on the cell surface for immune recognition. The majority of reported MHC-I peptides are derived from protein coding sequences, and noncanonical peptides translated from small open reading frames (sORF) are largely unknown due to the lack of accurate and sensitive detection methods. Herein we report an efficient approach that implements complementary bioinformatic strategies to improve the identification of noncanonical MHC-I peptides. In a database search strategy, noncanonical immunopeptides mapping was optimized by combining three complementary pipelines to construct predicted sORF databases from Ribo-seq data. In a de novo peptide sequencing strategy, MS data search results were filtered against sORF databases to pin down additional noncanonical immunopeptides. In total, 308 noncanonical immunopeptides were identified from two tumor cell lines with selected ones vigorously validated. Our approach is a handy solution to identify noncanonical MHC peptides with Ribo-seq and MS data. Meanwhile, the novel noncanonical immunopeptides identified with this method could shed insights on fundamental immunology as well as cancer immunotherapies.
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Affiliation(s)
- Lei Chen
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong SAR 999077, China
| | - Yuanliang Zhang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
| | - Ying Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
| | - Yang Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
| | - Huihui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518083, China
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
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30
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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: 57] [Impact Index Per Article: 19.0] [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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