1
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Huang J, Yang P, Pan W, Wu F, Qiu J, Ma Z. The role of polypeptides encoded by ncRNAs in cancer. Gene 2024; 928:148817. [PMID: 39098512 DOI: 10.1016/j.gene.2024.148817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/22/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
It was previously thought that ncRNA could not encode polypeptides, but recent reports have challenged this notion. As research into ncRNA progresses, it is increasingly clear that it serves roles beyond traditional mechanisms, playing significant regulatory roles in various diseases, notably cancer, which is responsible for 70% of human deaths. Numerous studies have highlighted the diverse regulatory mechanisms of ncRNA that are pivotal in cancer initiation and progression. The role of ncRNA-encoded polypeptides in cancer regulation has gained prominence. This article explores the newly identified regulatory functions of these polypeptides in three types of ncRNA-lncRNA, pri-miRNA, and circRNA. These polypeptides can interact with proteins, influence signaling pathways, enhance miRNA stability, and regulate cancer progression, malignancy, resistance, and other clinical challenges. Furthermore, we discuss the evolutionary significance of these polypeptides in the transition from RNA to protein, examining their emergence and conservation throughout evolution.
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Affiliation(s)
- Jiayuan Huang
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Ping Yang
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming 650118,China
| | - Wei Pan
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Fan Wu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jianhua Qiu
- Department of Anesthesiology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 201800, China.
| | - Zhongliang Ma
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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2
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Wen K, Chen X, Gu J, Chen Z, Wang Z. Beyond traditional translation: ncRNA derived peptides as modulators of tumor behaviors. J Biomed Sci 2024; 31:63. [PMID: 38877495 PMCID: PMC11177406 DOI: 10.1186/s12929-024-01047-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/24/2024] [Indexed: 06/16/2024] Open
Abstract
Within the intricate tapestry of molecular research, noncoding RNAs (ncRNAs) were historically overshadowed by a pervasive presumption of their inability to encode proteins or peptides. However, groundbreaking revelations have challenged this notion, unveiling select ncRNAs that surprisingly encode peptides specifically those nearing a succinct 100 amino acids. At the forefront of this epiphany stand lncRNAs and circRNAs, distinctively characterized by their embedded small open reading frames (sORFs). Increasing evidence has revealed different functions and mechanisms of peptides/proteins encoded by ncRNAs in cancer, including promotion or inhibition of cancer cell proliferation, cellular metabolism (glucose metabolism and lipid metabolism), and promotion or concerted metastasis of cancer cells. The discoveries not only accentuate the depth of ncRNA functionality but also open novel avenues for oncological research and therapeutic innovations. The main difficulties in the study of these ncRNA-derived peptides hinge crucially on precise peptide detection and sORFs identification. Here, we illuminate cutting-edge methodologies, essential instrumentation, and dedicated databases tailored for unearthing sORFs and peptides. In addition, we also conclude the potential of clinical applications in cancer therapy.
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Affiliation(s)
- Kang Wen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Jingyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Zhenyao Chen
- Department of Respiratory Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P.R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China.
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3
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Dasgupta A, Prensner JR. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer 2024; 6:zcae023. [PMID: 38774471 PMCID: PMC11106035 DOI: 10.1093/narcan/zcae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
The translation of RNA by ribosomes represents a central biological process and one of the most dysregulated processes in cancer. While translation is traditionally thought to occur exclusively in the protein-coding regions of messenger RNAs (mRNAs), recent transcriptome-wide approaches have shown abundant ribosome activity across diverse stretches of RNA transcripts. The most common type of this kind of ribosome activity occurs in gene leader sequences, also known as 5' untranslated regions (UTRs) of the mRNA, that precede the main coding sequence. Translation of these upstream open reading frames (uORFs) is now known to occur in upwards of 25% of all protein-coding genes. With diverse functions from RNA regulation to microprotein generation, uORFs are rapidly igniting a new arena of cancer biology, where they are linked to cancer genetics, cancer signaling, and tumor-immune interactions. This review focuses on the contributions of uORFs and their associated 5'UTR sequences to cancer biology.
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Affiliation(s)
- Anwesha Dasgupta
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John R Prensner
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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4
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Qin Z, Yang J, Zhang K, Gao X, Ran Q, Xu Y, Wang Z, Lou D, Huang C, Zellmer L, Meng G, Chen N, Ma H, Wang Z, Liao DJ. Updating mRNA variants of the human RSK4 gene and their expression in different stressed situations. Heliyon 2024; 10:e27475. [PMID: 38560189 PMCID: PMC10980951 DOI: 10.1016/j.heliyon.2024.e27475] [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: 01/20/2024] [Revised: 02/11/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
We determined RNA spectrum of the human RSK4 (hRSK4) gene (also called RPS6KA6) and identified 29 novel mRNA variants derived from alternative splicing, which, plus the NCBI-documented ones and the five we reported previously, totaled 50 hRSK4 RNAs that, by our bioinformatics analyses, encode 35 hRSK4 protein isoforms of 35-762 amino acids. Many of the mRNAs are bicistronic or tricistronic for hRSK4. The NCBI-normalized NM_014496.5 and the protein it encodes are designated herein as the Wt-1 mRNA and protein, respectively, whereas the NM_001330512.1 and the long protein it encodes are designated as the Wt-2 mRNA and protein, respectively. Many of the mRNA variants responded differently to different situations of stress, including serum starvation, a febrile temperature, treatment with ethanol or ethanol-extracted clove buds (an herbal medicine), whereas the same stressed situation often caused quite different alterations among different mRNA variants in different cell lines. Mosifloxacin, an antibiotics and also a functional inhibitor of hRSK4, could inhibit the expression of certain hRSK4 mRNA variants. The hRSK4 gene likely uses alternative splicing as a handy tool to adapt to different stressed situations, and the mRNA and protein multiplicities may partly explain the incongruous literature on its expression and comports.
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Affiliation(s)
- Zhenwei Qin
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Jianglin Yang
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Rd, Guiyang, 550004, Guizhou Province, China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
| | - Keyin Zhang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Xia Gao
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Qianchuan Ran
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Yuanhong Xu
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Zhi Wang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Didong Lou
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Chunhua Huang
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Lucas Zellmer
- Department of Medicine, Hennepin County Medical Center, 730 South 8th St., Minneapolis, MN, 55415, USA
| | - Guangxue Meng
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Na Chen
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Hong Ma
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Zhe Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Air Force Medical University, 169 Changle West Road, Xi'an, 710032, China
| | - Dezhong Joshua Liao
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Rd, Guiyang, 550004, Guizhou Province, China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
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Zhang Q, Liu L. Novel insights into small open reading frame-encoded micropeptides in hepatocellular carcinoma: A potential breakthrough. Cancer Lett 2024; 587:216691. [PMID: 38360139 DOI: 10.1016/j.canlet.2024.216691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/13/2024] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Traditionally, non-coding RNAs (ncRNAs) are regarded as a class of RNA transcripts that lack encoding capability; however, advancements in technology have revealed that some ncRNAs contain small open reading frames (sORFs) that are capable of encoding micropeptides of approximately 150 amino acids in length. sORF-encoded micropeptides (SEPs) have emerged as intriguing entities in hepatocellular carcinoma (HCC) research, shedding light on this previously unexplored realm. Recent studies have highlighted the regulatory functions of SEPs in the occurrence and progression of HCC. Some SEPs exhibit inhibitory effects on HCC, but others facilitate its development. This discovery has revolutionized the landscape of HCC research and clinical management. Here, we introduce the concept and characteristics of SEPs, summarize their associations with HCC, and elucidate their carcinogenic mechanisms in HCC metabolism, signaling pathways, cell proliferation, and metastasis. In addition, we propose a step-by-step workflow for the investigation of HCC-associated SEPs. Lastly, we discuss the challenges and prospects of applying SEPs in the diagnosis and treatment of HCC. This review aims to facilitate the discovery, optimization, and clinical application of HCC-related SEPs, inspiring the development of early diagnostic, individualized, and precision therapeutic strategies for HCC.
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Affiliation(s)
- Qiangnu Zhang
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
| | - Liping Liu
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China.
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Shi L, Feng G, Yang X, Zhang Y, Zhang Y, Cheng J, Lin S. Potential of PAQosome as a therapeutic target for hepatic fibrosis. J Gastroenterol Hepatol 2024; 39:381-391. [PMID: 38016755 DOI: 10.1111/jgh.16427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND AND AIM The condition of hepatic fibrosis is hazardous. Therefore, it is vital that we investigate the mechanism of hepatic fibrosis to provide new targets for treatment. METHODS Preliminary screening and research was carried out based on our prior results and our speculated role of the particle with quaternary structure arrangement (PAQosome) in hepatic fibrosis. The experiments were conducted using LX-2 or HepG2 cell lines by western blotting, quantitative real-time polymerase chain reaction, luciferase assays, and co-immunoprecipitation and were further validated in the Gene Expression Omnibus (GEO) database. RESULTS We screened and proved that several subunits of the PAQosome regulate the development of liver fibrosis, including the asparagine synthetase domain-containing 1 upstream open reading frame (ASDURF), prefoldin subunit 4 (PFDN4), prefoldin subunit 5 (PFDN5), unconventional prefoldin RNA polymerase II subunit 5 interactor (URI1), and ubiquitously expressed prefoldin-like chaperone (UXT). ASDURF promotes hepatic fibrosis through the transforming growth factor-β1 (TGFβ1)/Sekelsky mothers against decapentaplegic homologue 3 (Smad3) and NF-κB signaling pathways. ASDURF regulates the expression of asparagine synthetase domain-containing 1 (ASNSD1). PFDN4, PFDN5, URI1, and UXT regulate cell proliferation through the PI3K/AKT pathway, and thus regulate liver fibrosis. A hepatic fibrosis score ≥ F2 was selected as the diagnostic criteria for hepatic fibrosis in the GSE96971 database. The area under the receiver operating characteristic curve of PFDN4, PFDN5, UXT, and ASNSD1 were 0.862 (confidence interval [CI]: 0.6588-1.000), 0.538 (CI: 0.224-0.853), 0.708 (CI: 0.449-0.966), and 0.831 (CI: 0.638-1.000), respectively. CONCLUSIONS These findings demonstrate that the PAQosome is a brand new target for hepatic fibrosis therapy.
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Affiliation(s)
- Liu Shi
- Department of Infectious Disease Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Gong Feng
- Department of Infectious Disease Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Xi'an Medical University, Xi'an, China
| | - Xueliang Yang
- Department of Rehabilitation Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yang Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yu Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jun Cheng
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shumei Lin
- Department of Infectious Disease Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Zhang L, Tang M, Diao H, Xiong L, Yang X, Xing S. LncRNA-encoded peptides: unveiling their significance in cardiovascular physiology and pathology-current research insights. Cardiovasc Res 2023; 119:2165-2178. [PMID: 37517040 DOI: 10.1093/cvr/cvad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/17/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), which are RNA transcripts exceeding 200 nucleotides were believed to lack any protein-coding capacity. But advancements in -omics technology have revealed that some lncRNAs have small open reading frames (sORFs) that can be translated by ribosomes to encode peptides, some of which have important biological functions. These encoded peptides subserve important biological functions by interacting with their targets to modulate transcriptional or signalling axes, thereby enhancing or suppressing cardiovascular disease (CVD) occurrence and progression. In this review, we summarize what is known about the research strategy of lncRNA-encoded peptides, mainly comprising predictive websites/tools and experimental methods that have been widely used for prediction, identification, and validation. More importantly, we have compiled a list of lncRNA- encoded peptides, with a focus on those that play significant roles in cardiovascular physiology and pathology, including ENSRNOT (RNO)-sORF6/RNO-sORF7/RNO-sORF8, dwarf open reading frame (DOWRF), myoregulin (NLN), etc. Additionally, we have outlined the functions and mechanisms of these peptides in cardiovascular physiology and pathology, such as cardiomyocyte hypertrophy, myocardial contraction, myocardial infarction, and vascular remodelling. Finally, an overview of the existing challenges and potential future developments in the realm of lncRNA-encoded peptides was provided, with consideration given to prospective avenues for further research. Given that many lncRNA-encoded peptides have not been functionally annotated yet, their application in CVD diagnosis and treatment still requires further research.
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Affiliation(s)
- Li Zhang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Mi Tang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Haoyang Diao
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Liling Xiong
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Xiao Yang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Shasha Xing
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
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Ventroux M, Noirot-Gros MF. Prophage-encoded small protein YqaH counteracts the activities of the replication initiator DnaA in Bacillus subtilis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748575 DOI: 10.1099/mic.0.001268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacterial genomes harbour cryptic prophages that are mostly transcriptionally silent with many unannotated genes. Still, cryptic prophages may contribute to their host fitness and phenotypes. In Bacillus subtilis, the yqaF-yqaN operon belongs to the prophage element skin, and is tightly repressed by the Xre-like repressor SknR. This operon contains several small ORFs (smORFs) potentially encoding small-sized proteins. The smORF-encoded peptide YqaH was previously reported to bind to the replication initiator DnaA. Here, using a yeast two-hybrid assay, we found that YqaH binds to the DNA binding domain IV of DnaA and interacts with Spo0A, a master regulator of sporulation. We isolated single amino acid substitutions in YqaH that abolished the interaction with DnaA but not with Spo0A. Then, using a plasmid-based inducible system to overexpress yqaH WT and mutant derivatives, we studied in B. subtilis the phenotypes associated with the specific loss-of-interaction with DnaA (DnaA_LOI). We found that expression of yqaH carrying DnaA_LOI mutations abolished the deleterious effects of yqaH WT expression on chromosome segregation, replication initiation and DnaA-regulated transcription. When YqaH was induced after vegetative growth, DnaA_LOI mutations abolished the drastic effects of YqaH WT on sporulation and biofilm formation. Thus, YqaH inhibits replication, sporulation and biofilm formation mainly by antagonizing DnaA in a manner that is independent of the cell cycle checkpoint Sda.
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Affiliation(s)
- Magali Ventroux
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Yuanyuan J, Xinqiang Y. Micropeptides Identified from Human Genomes. J Proteome Res 2022; 21:865-873. [DOI: 10.1021/acs.jproteome.1c00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Yuanyuan
- School of Public Health, North Sichuan Medical College, Nanchong 637000, China
| | - Yin Xinqiang
- School of Basic Medicine and Forensics, North Sichuan Medical College, Nanchong 637000, China
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10
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Small open reading frames in plant research: from prediction to functional characterization. 3 Biotech 2022; 12:76. [PMID: 35251879 PMCID: PMC8873315 DOI: 10.1007/s13205-022-03147-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/11/2022] [Indexed: 11/01/2022] Open
Abstract
Gene prediction is a laborious and time-consuming task. The advancement of sequencing technologies and bioinformatics tools, coupled with accelerated rate of ribosome profiling and mass spectrometry development, have made identification of small open reading frames (sORFs) (< 100 codons) in various plant genomes possible. The past 50 years have seen sORFs being isolated from many organisms. However, to date, a comprehensive sORF annotation pipeline is as yet unavailable, hence, addressed in our review. Here, we also provide current information on classification and functions of plant sORFs and their potential applications in crop improvement programs.
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Abstract
In recent years, there has been increased appreciation that a whole category of proteins, small proteins of around 50 amino acids or fewer in length, has been missed by annotation as well as by genetic and biochemical assays. With the increased recognition that small proteins are stable within cells and have regulatory functions, there has been intensified study of these proteins. As a result, important questions about small proteins in bacteria and archaea are coming to the fore. Here, we give an overview of these questions, the initial answers, and the approaches needed to address these questions more fully. More detailed discussions of how small proteins can be identified by ribosome profiling and mass spectrometry approaches are provided by two accompanying reviews (N. Vazquez-Laslop, C. M. Sharma, A. S. Mankin, and A. R. Buskirk, J Bacteriol 204:e00294-21, 2022, https://doi.org/10.1128/JB.00294-21; C. H. Ahrens, J. T. Wade, M. M. Champion, and J. D. Langer, J Bacteriol 204:e00353-21, 2022, https://doi.org/10.1128/JB.00353-21). We are excited by the prospects of new insights and possible therapeutic approaches coming from this emerging field.
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Affiliation(s)
- Todd Gray
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Microverse Cluster, Friedrich Schiller University, Jena, Germany
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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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13
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Parmar BS, Peeters MKR, Boonen K, Clark EC, Baggerman G, Menschaert G, Temmerman L. Identification of Non-Canonical Translation Products in C. elegans Using Tandem Mass Spectrometry. Front Genet 2021; 12:728900. [PMID: 34759956 PMCID: PMC8575065 DOI: 10.3389/fgene.2021.728900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022] Open
Abstract
Transcriptome and ribosome sequencing have revealed the existence of many non-canonical transcripts, mainly containing splice variants, ncRNA, sORFs and altORFs. However, identification and characterization of products that may be translated out of these remains a challenge. Addressing this, we here report on 552 non-canonical proteins and splice variants in the model organism C. elegans using tandem mass spectrometry. Aided by sequencing-based prediction, we generated a custom proteome database tailored to search for non-canonical translation products of C. elegans. Using this database, we mined available mass spectrometric resources of C. elegans, from which 51 novel, non-canonical proteins could be identified. Furthermore, we utilized diverse proteomic and peptidomic strategies to detect 40 novel non-canonical proteins in C. elegans by LC-TIMS-MS/MS, of which 6 were common with our meta-analysis of existing resources. Together, this permits us to provide a resource with detailed annotation of 467 splice variants and 85 novel proteins mapped onto UTRs, non-coding regions and alternative open reading frames of the C. elegans genome.
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Affiliation(s)
- Bhavesh S. Parmar
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Marlies K. R. Peeters
- Laboratory of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Kurt Boonen
- Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium
| | - Ellie C. Clark
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Geert Baggerman
- Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium
| | - Gerben Menschaert
- Laboratory of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
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14
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Zhao S, Meng J, Luan Y. LncRNA-Encoded Short Peptides Identification Using Feature Subset Recombination and Ensemble Learning. Interdiscip Sci 2021; 14:101-112. [PMID: 34304369 DOI: 10.1007/s12539-021-00464-1] [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: 03/24/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 11/28/2022]
Abstract
Long non-coding RNA (lncRNA), which is a type of non-coding RNA, was reported to contain short open reading frames (sORFs). SORFs-encoded short peptides (SEPs) have been demonstrated to play a crucial role in regulating the biological processes such as growth, development, and resistance response. The identification of SEPs is vital to further understanding their function. However, there is still a lack of methods for identifying SEPs effectively and rapidly. In this study, a novel method for lncRNA-encoded short peptides identification based on feature subset recombination and ensemble learning, lncPepid, is developed. lncPepid transforms the data of Zea mays and Arabidopsis thaliana into hybrid features from two aspects including sequence composition and physicochemical properties separately. It optimizes hybrid features by proposing a novel weighted iteration-based feature selection method to recombine a stable subset that characterizes SEPs effectively. Different classification models with different optimized features are constructed and tested separately. The outputs of the optimal models are integrated for ensemble classification to improve efficiency. Experimental results manifest that the geometric mean of sensitivity and specificity of lncPepid is about 70% on the identification of functional SEPs derived from multiple species. It is an effective and rapid method for the identification of lncRNA-encoded short peptides. This study can be extended to the research on SEPs from other species and have crucial implications for further findings and studies of functional genomics.
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Affiliation(s)
- Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
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15
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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: 15] [Impact Index Per Article: 5.0] [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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16
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Gao X, Zhang K, Zhou H, Zellmer L, Yuan C, Huang H, Liao DJ. At elevated temperatures, heat shock protein genes show altered ratios of different RNAs and expression of new RNAs, including several novel HSPB1 mRNAs encoding HSP27 protein isoforms. Exp Ther Med 2021; 22:900. [PMID: 34257713 PMCID: PMC8243336 DOI: 10.3892/etm.2021.10332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/10/2021] [Indexed: 12/22/2022] Open
Abstract
Heat shock proteins (HSP) serve as chaperones to maintain the physiological conformation and function of numerous cellular proteins when the ambient temperature is increased. To determine how accurate the general assumption that HSP gene expression is increased in febrile situations is, the RNA levels of the HSF1 (heat shock transcription factor 1) gene and certain HSP genes were determined in three cell lines cultured at 37˚C or 39˚C for three days. At 39˚C, the expression of HSF1, HSPB1, HSP90AA1 and HSP70A1L genes demonstrated complex changes in the ratios of expression levels between different RNA variants of the same gene. Several older versions of the RNAs of certain HSP genes that have been replaced by a newer version in the National Center for Biotechnology Information database were also detected, indicating that the older versions are actually RNA variants of these genes. The present study cloned four new RNA variants of the HSP27-encoding HSPB1 gene, which together encode three short HSP27 peptides. Reanalysis of the proteomics data from our previous studies also demonstrated that proteins from certain HSP genes could be detected simultaneously at multiple positions using SDS-PAGE, suggesting that these genes may engender multiple protein isoforms. These results collectively suggested that, besides increasing their expression, certain HSP and associated genes also use alternative transcription start sites to produce multiple RNA transcripts and use alternative splicing of a transcript to produce multiple mature RNAs, as important mechanisms for responding to an increased ambient temperature in vitro.
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Affiliation(s)
- Xia Gao
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China.,Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Keyin Zhang
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China.,Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Haiyan Zhou
- Clinical Research Center, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
| | - Lucas Zellmer
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Hai Huang
- Center for Clinical Laboratories, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
| | - Dezhong Joshua Liao
- Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Center for Clinical Laboratories, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
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17
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Abstract
Recent technological advances have expanded the annotated protein coding content of mammalian genomes, as hundreds of previously unidentified, short open reading frame (ORF)-encoded peptides (SEPs) have now been found to be translated. Although several studies have identified important physiological roles for this emerging protein class, a general method to define their interactomes is lacking. Here, we demonstrate that genetic incorporation of the photo-crosslinking noncanonical amino acid AbK into SEP transgenes allows for the facile identification of SEP cellular interaction partners using affinity-based methods. From a survey of seven SEPs, we report the discovery of short ORF-encoded histone binding protein (SEHBP), a conserved microprotein that interacts with chromatin-associated proteins, localizes to discrete genomic loci, and induces a robust transcriptional program when overexpressed in human cells. This work affords a straightforward method to help define the physiological roles of SEPs and demonstrates its utility by identifying SEHBP as a short ORF-encoded transcription factor.
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18
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Vitorino R, Guedes S, Amado F, Santos M, Akimitsu N. The role of micropeptides in biology. Cell Mol Life Sci 2021; 78:3285-3298. [PMID: 33507325 PMCID: PMC11073438 DOI: 10.1007/s00018-020-03740-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
Abstract
Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.
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Affiliation(s)
- Rui Vitorino
- Departamento de Cirurgia E Fisiologia, Faculdade de Medicina da Universidade Do Porto, UnIC, Porto, Portugal.
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal.
| | - Sofia Guedes
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manuel Santos
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal
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19
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Morris DL, Tjandra N. Inducible fold-switching as a mechanism to fibrillate pro-apoptotic BCL-2 proteins. Biopolymers 2021; 112:e23424. [PMID: 33764501 DOI: 10.1002/bip.23424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/18/2021] [Accepted: 03/05/2021] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases often are associated with cellular dysregulation that results in premature cell death or apoptosis. A common example is the accumulation of amyloid plaques that promotes the excessive expression of p38 mitogen-activated protein kinase. The increased abundance of this enzyme leads to mass phosphorylation and activation of a protein from the B-cell lymphoma 2 (BCL-2) family, BAX. BAX is the central regulatory protein for mitochondrial outer membrane permeabilization (MOMP), a poration process that commits cells to apoptosis by releasing death-propagating factors from the mitochondria. Recent reports identify a naturally occurring peptide, Humanin (HN), that could block amyloid-beta-associated neuronal apoptosis by interacting with BCL-2 proteins. We recently showed humanin interaction leads to the amyloid-like fibrillation of BAX and a second BCL-2 family member, BID. We proposed this as a novel anti-apoptotic mechanism that inhibits pro-apoptotic BCL-2 proteins from initiating MOMP by sequestering them into fibrils, a heretofore unprecedented phenomenon that involves refolding globular BCL-2 proteins rapidly into fibrils where they undergo significant alpha-helix to beta-sheet fold-switching. Here we seek to further characterize the fibrillation and fold-switch in conditions that are known to induce amyloid fibrillation.
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Affiliation(s)
- Daniel L Morris
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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20
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Gutt M, Jordan B, Weidenbach K, Gudzuhn M, Kiessling C, Cassidy L, Helbig A, Tholey A, Pyper DJ, Kubatova N, Schwalbe H, Schmitz RA. High complexity of Glutamine synthetase regulation in
Methanosarcina mazei
: Small protein 26 interacts and enhances glutamine synthetase activity. FEBS J 2021; 288:5350-5373. [DOI: 10.1111/febs.15799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/05/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Miriam Gutt
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Britta Jordan
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Katrin Weidenbach
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Mirja Gudzuhn
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Claudia Kiessling
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Andreas Helbig
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Andreas Tholey
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Dennis Joshua Pyper
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Nina Kubatova
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Ruth Anne Schmitz
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
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21
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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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22
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Fabre B, Combier JP, Plaza S. Recent advances in mass spectrometry-based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions. Curr Opin Chem Biol 2021; 60:122-130. [PMID: 33401134 DOI: 10.1016/j.cbpa.2020.12.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022]
Abstract
Short open reading frame (sORF)-encoded polypeptides (SEPs) have recently emerged as key regulators of major cellular processes. Computational methods for the annotation of sORFs combined with transcriptomics and ribosome profiling approaches predicted the existence of tens of thousands of SEPs across the kingdom of life. Although, we still lack unambiguous evidence for most of them. The method of choice to validate the expression of SEPs is mass spectrometry (MS)-based peptidomics. Peptides are less abundant than proteins, which tends to hinder their detection. Therefore, optimization and enrichment methods are necessary to validate the existence of SEPs. In this article, we discuss the challenges for the detection of SEPs by MS and recent developments of biochemical approaches applied to the study of these peptides. We detail the advances made in the different key steps of a typical peptidomics workflow and highlight possible alternatives that have not been explored yet.
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Affiliation(s)
- Bertrand Fabre
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France.
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, CNRS, 31320, Auzeville-Tolosane, France
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23
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Morris DL, Johnson S, Bleck CKE, Lee DY, Tjandra N. Humanin selectively prevents the activation of pro-apoptotic protein BID by sequestering it into fibers. J Biol Chem 2020; 295:18226-18238. [PMID: 33106313 DOI: 10.1074/jbc.ra120.013023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 10/23/2020] [Indexed: 03/01/2024] Open
Abstract
Members of the B-cell lymphoma (BCL-2) protein family regulate mitochondrial outer membrane permeabilization (MOMP), a phenomenon in which mitochondria become porous and release death-propagating complexes during the early stages of apoptosis. Pro-apoptotic BCL-2 proteins oligomerize at the mitochondrial outer membrane during MOMP, inducing pore formation. Of current interest are endogenous factors that can inhibit pro-apoptotic BCL-2 mitochondrial outer membrane translocation and oligomerization. A mitochondrial-derived peptide, Humanin (HN), was reported being expressed from an alternate ORF in the mitochondrial genome and inhibiting apoptosis through interactions with the pro-apoptotic BCL-2 proteins. Specifically, it is known to complex with BAX and BID. We recently reported the fibrillation of HN and BAX into β-sheets. Here, we detail the fibrillation between HN and BID. These fibers were characterized using several spectroscopic techniques, protease fragmentation with mass analysis, and EM. Enhanced fibrillation rates were detected with rising temperatures or pH values and the presence of a detergent. BID fibers are similar to those produced using BAX; however, the structures differ in final conformations of the BCL-2 proteins. BID fibers display both types of secondary structure in the fiber, whereas BAX was converted entirely to β-sheets. The data show that two distinct segments of BID are incorporated into the fiber structure, whereas other portions of BID remain solvent-exposed and retain helical structure. Similar analyses show that anti-apoptotic BCL-xL does not form fibers with humanin. These results support a general mechanism of sequestration of pro-apoptotic BCL-2 proteins into fibers by HN to inhibit MOMP.
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Affiliation(s)
- Daniel L Morris
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Sabrina Johnson
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Christopher K E Bleck
- Electron Microscopy Core Facility, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Duck-Yeon Lee
- Biochemistry Core Facility, NHLBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland, USA.
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24
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Kaulich PT, Cassidy L, Weidenbach K, Schmitz RA, Tholey A. Complementarity of Different SDS‐PAGE Gel Staining Methods for the Identification of Short Open Reading Frame‐Encoded Peptides. Proteomics 2020; 20:e2000084. [DOI: 10.1002/pmic.202000084] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/15/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Philipp T. Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine Christian‐Albrechts‐Universität zu Kiel Kiel 24105 Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine Christian‐Albrechts‐Universität zu Kiel Kiel 24105 Germany
| | - Katrin Weidenbach
- Institute for General Microbiology Christian‐Albrechts‐Universität zu Kiel Kiel 24118 Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology Christian‐Albrechts‐Universität zu Kiel Kiel 24118 Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine Christian‐Albrechts‐Universität zu Kiel Kiel 24105 Germany
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25
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Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, Göbel M, Döring K, Menegatti J, Antrobus R, Matheson NJ, Künzig FWH, Mastrobuoni G, Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R, Landthaler M, Grässer F, Lehner PJ, Friedel CC, Erhard F, Dölken L. Integrative functional genomics decodes herpes simplex virus 1. Nat Commun 2020; 11:2038. [PMID: 32341360 PMCID: PMC7184758 DOI: 10.1038/s41467-020-15992-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/06/2020] [Indexed: 12/15/2022] Open
Abstract
The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution.
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Affiliation(s)
- Adam W Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Christopher S Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Bhupesh Prusty
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Andrzej J Rutkowski
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, CB2 0QQ, Cambridge, UK
| | - Anne L'hernault
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, CB2 0QQ, Cambridge, UK
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Margarete Göbel
- Core Unit Systems Medicine, Julius-Maximilians-University Würzburg, Josef-Schneider-Str. 2/D15, 97080, Würzburg, Germany
| | - Kristina Döring
- Core Unit Systems Medicine, Julius-Maximilians-University Würzburg, Josef-Schneider-Str. 2/D15, 97080, Würzburg, Germany
| | - Jennifer Menegatti
- Institute of Virology, Building 47, Saarland University Medical School, 66421, Homburg, Saar, Germany
| | - Robin Antrobus
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Florian W H Künzig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Guido Mastrobuoni
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Chris Bielow
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Stefan Kempa
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Chunguang Liang
- Department of Bioinformatics, Biocenter, Am Hubland, Julius-Maximilians-University Würzburg, 97074, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, Julius-Maximilians-University Würzburg, 97074, Würzburg, Germany
| | - Ralf Zimmer
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Friedrich Grässer
- Institute of Virology, Building 47, Saarland University Medical School, 66421, Homburg, Saar, Germany
| | - Paul J Lehner
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany.
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany.
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, CB2 0QQ, Cambridge, UK.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), 97080, Würzburg, Germany.
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Peng J, Zhang H, Niu H, Wu R. Peptidomic analyses: The progress in enrichment and identification of endogenous peptides. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115835] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Vassallo A, Palazzotto E, Renzone G, Botta L, Faddetta T, Scaloni A, Puglia AM, Gallo G. The Streptomyces coelicolor Small ORF trpM Stimulates Growth and Morphological Development and Exerts Opposite Effects on Actinorhodin and Calcium-Dependent Antibiotic Production. Front Microbiol 2020; 11:224. [PMID: 32140146 PMCID: PMC7042404 DOI: 10.3389/fmicb.2020.00224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/30/2020] [Indexed: 11/25/2022] Open
Abstract
In actinomycetes, antibiotic production is often associated with a morpho-physiological differentiation program that is regulated by complex molecular and metabolic networks. Many aspects of these regulatory circuits have been already elucidated and many others still deserve further investigations. In this regard, the possible role of many small open reading frames (smORFs) in actinomycete morpho-physiological differentiation is still elusive. In Streptomyces coelicolor, inactivation of the smORF trpM (SCO2038) – whose product modulates L-tryptophan biosynthesis – impairs production of antibiotics and morphological differentiation. Indeed, it was demonstrated that TrpM is able to interact with PepA (SCO2179), a putative cytosol aminopeptidase playing a key role in antibiotic production and sporulation. In this work, a S. coelicolor trpM knock-in (Sco-trpMKI) mutant strain was generated by cloning trpM into overexpressing vector to further investigate the role of trpM in actinomycete growth and morpho-physiological differentiation. Results highlighted that trpM: (i) stimulates growth and actinorhodin (ACT) production; (ii) decreases calcium-dependent antibiotic (CDA) production; (iii) has no effect on undecylprodigiosin production. Metabolic pathways influenced by trpM knock-in were investigated by combining two-difference in gel electrophoresis/nanoliquid chromatography coupled to electrospray linear ion trap tandem mass spectrometry (2D-DIGE/nanoLC-ESI-LIT-MS/MS) and by LC-ESI-MS/MS procedures, respectively. These analyses demonstrated that over-expression of trpM causes an over-representation of factors involved in protein synthesis and nucleotide metabolism as well as a down-representation of proteins involved in central carbon and amino acid metabolism. At the metabolic level, this corresponded to a differential accumulation pattern of different amino acids – including aromatic ones but tryptophan – and central carbon intermediates. PepA was also down-represented in Sco-trpMKI. The latter was produced as recombinant His-tagged protein and was originally proven having the predicted aminopeptidase activity. Altogether, these results highlight the stimulatory effect of trpM in S. coelicolor growth and ACT biosynthesis, which are elicited through the modulation of various metabolic pathways and PepA representation, further confirming the complexity of regulatory networks that control antibiotic production in actinomycetes.
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Affiliation(s)
- Alberto Vassallo
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy.,Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Emilia Palazzotto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Giovanni Renzone
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Luigi Botta
- Dipartimento di Ingegneria, Università di Palermo, Palermo, Italy
| | - Teresa Faddetta
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
| | - Andrea Scaloni
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
| | - Giuseppe Gallo
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
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Huo LJ, Yang MC, Wang JX, Shi XZ. Mitochondrial ATPase inhibitor factor 1, MjATPIF1, is beneficial for WSSV replication in kuruma shrimp (Marsupenaeus japonicus). FISH & SHELLFISH IMMUNOLOGY 2020; 98:245-254. [PMID: 31945484 DOI: 10.1016/j.fsi.2020.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/05/2020] [Accepted: 01/12/2020] [Indexed: 06/10/2023]
Abstract
ATPase Inhibitory Factor 1 (IF1) is a mitochondrial protein that functions as a physiological inhibitor of F1F0-ATP synthase. In the present study, a mitochondrial ATPase inhibitor factor 1 (MjATPIF1) was identified from kuruma shrimp (Marsupenaeus japonicus), which was demonstrated to participate in the viral immune reaction of white spot syndrome virus (WSSV). MjATPIF1 contained a mitochondrial ATPase inhibitor (IATP) domain, and was widely distributed in hemocytes, heart, hepatopancreas, gills, stomach, and intestine of shrimp. MjATPIF1 transcription was upregulated in hemocytes and intestines by WSSV. WSSV replication decreased after MjATPIF1 knockdown by RNA interference and increased following recombinant MjATPIF1 protein injection. Further study found that MjATPIF1 promoted the production of superoxide and activated the transcription factor nuclear factor kappa B (NF-κB, Dorsal) to induce the transcription of WSSV RNAs. These results demonstrate that MjATPIF1 benefits WSSV replication in kuruma shrimp by inducing superoxide production and NF-κB activation.
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Affiliation(s)
- Li-Jie Huo
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Ming-Chong Yang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiu-Zhen Shi
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China.
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29
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Yang J, Moraga A, Xu J, Zhao Y, Luo P, Lao KH, Margariti A, Zhao Q, Ding W, Wang G, Zhang M, Zheng L, Zhang Z, Hu Y, Wang W, Shen L, Smith A, Shah AM, Wang Q, Zeng L. A histone deacetylase 7-derived peptide promotes vascular regeneration via facilitating 14-3-3γ phosphorylation. Stem Cells 2020; 38:556-573. [PMID: 31721359 PMCID: PMC7187271 DOI: 10.1002/stem.3122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022]
Abstract
Histone deacetylase 7 (HDAC7) plays a pivotal role in the maintenance of the endothelium integrity. In this study, we demonstrated that the intron-containing Hdac7 mRNA existed in the cytosol and that ribosomes bound to a short open reading frame (sORF) within the 5'-terminal noncoding area of this Hdac7 mRNA in response to vascular endothelial growth factor (VEGF) stimulation in the isolated stem cell antigen-1 positive (Sca1+ ) vascular progenitor cells (VPCs). A 7-amino acid (7A) peptide has been demonstrated to be translated from the sORF in Sca1+ -VPCs in vitro and in vivo. The 7A peptide was shown to receive phosphate group from the activated mitogen-activated protein kinase MEKK1 and transfer it to 14-3-3 gamma protein, forming an MEKK1-7A-14-3-3γ signal pathway downstream VEGF. The exogenous synthetic 7A peptide could increase Sca1+ -VPCs cell migration, re-endothelialization in the femoral artery injury, and angiogenesis in hind limb ischemia. A Hd7-7sFLAG transgenic mice line was generated as the loss-of-function model, in which the 7A peptide was replaced by a FLAG-tagged scrabbled peptide. Loss of the endogenous 7A impaired Sca1+ -VPCs cell migration, re-endothelialization of the injured femoral artery, and angiogenesis in ischemic tissues, which could be partially rescued by the addition of the exogenous 7A/7Ap peptide. This study provides evidence that sORFs can be alternatively translated and the derived peptides may play an important role in physiological processes including vascular remodeling.
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Affiliation(s)
- Junyao Yang
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK.,Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Ana Moraga
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Jing Xu
- Institute of Bioengineering, Queen Mary University of London, London, UK
| | - Yue Zhao
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Peiyi Luo
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Ka Hou Lao
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Andriana Margariti
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Qiang Zhao
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - Wei Ding
- Institute of Bioengineering, Queen Mary University of London, London, UK
| | - Gang Wang
- Department of Emergency Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Min Zhang
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Lei Zheng
- Southern Medical University, Guangzhou, People's Republic of China
| | - Zhongyi Zhang
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Yanhua Hu
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Wen Wang
- Institute of Bioengineering, Queen Mary University of London, London, UK
| | - Lisong Shen
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Alberto Smith
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Ajay M Shah
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Qian Wang
- Southern Medical University, Guangzhou, People's Republic of China
| | - Lingfang Zeng
- School of Cardiovascular Medicine and Sciences, King's College - London British Heart Foundation Centre of Excellence, Faculty of Life Science and Medicine, King's College London, London, UK
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30
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Qu J, Zhang J, Zellmer L, He Y, Liu S, Wang C, Yuan C, Xu N, Huang H, Liao DJ. About three-fourths of mouse proteins unexpectedly appear at a low position of SDS-PAGE, often as additional isoforms, questioning whether all protein isoforms have been eliminated in gene-knockout cells or organisms. Protein Sci 2020; 29:978-990. [PMID: 31930537 DOI: 10.1002/pro.3823] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/01/2020] [Accepted: 01/05/2020] [Indexed: 01/08/2023]
Abstract
Most genes in evolutionarily complex genomes are expressed to multiple protein isoforms, but there is not yet any simple high-throughput approach to identify these isoforms. Using an oversimplified top-down LC-MS/MS strategy, we detected, around the 26-kD position of SDS-PAGE, proteins produced from 782 genes in a Cdk4-/- mouse embryonic fibroblast cell line. Interestingly, only 213 (27.24%, about one-fourth) of these 782 genes have their proteins with a theoretical molecular mass (TMM) 10% smaller or larger than 26 kD, that is, between 23 and 29 kD, the range set as allowed variation in SDS-PAGE. These 213 proteins are considered as the wild type (WT). The remaining three-fourths includes proteins from 66 (9.44%) genes with a TMM smaller than 23 kD and proteins from 503 (64.32%, nearly two-thirds) genes with a TMM larger than 29 kD; these proteins are categorized into a larger-group or a smaller-group, respectively, for their appearance at a higher or lower position of SDS-PAGE. For instance, at this 26-kD position we detected proteins from the Rps27a, Snrpf, Hist1h4a, and Rps25 genes whose proteins' TMM is 8.6, 9.7, 11.4, and 13.7 kD, respectively, and detected proteins from the Plelc1 and Prkdc genes, whose largest isoform is 533.9 and 471.1 kD, respectively. We extrapolate that many of those proteins migrating unexpectedly in SDS-PAGE may be isoforms besides the WT protein. Moreover, we also detected a Cdk4 protein in this Cdk4-/- cell line, thus wondering whether some of other gene-knockout cells or organisms show similar incompleteness of the knockout.
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Affiliation(s)
- Jiayuan Qu
- Department of Biochemistry, China Three Gorges University, Yichang, Hubei Province, China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lucas Zellmer
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Yan He
- Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou Province, P. R., China
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | | | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang, Hubei Province, China
| | - Ningzhi Xu
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hai Huang
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Dezhong J Liao
- Laboratory for Core Facilities, The Second Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou Province, China
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31
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Cloutier P, Poitras C, Faubert D, Bouchard A, Blanchette M, Gauthier MS, Coulombe B. Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome. J Proteome Res 2019; 19:18-27. [PMID: 31738558 DOI: 10.1021/acs.jproteome.9b00599] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The PAQosome is an 11-subunit chaperone involved in the biogenesis of several human protein complexes. We show that ASDURF, a recently discovered upstream open reading frame (uORF) in the 5' UTR of ASNSD1 mRNA, encodes the 12th subunit of the PAQosome. ASDURF displays significant structural homology to β-prefoldins and assembles with the five known subunits of the prefoldin-like module of the PAQosome to form a heterohexameric prefoldin-like complex. A model of the PAQosome prefoldin-like module is presented. The data presented here provide an example of a eukaryotic uORF-encoded polypeptide whose function is not limited to cis-acting translational regulation of downstream coding sequence and highlights the importance of including alternative ORF products in proteomic studies.
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Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Christian Poitras
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Annie Bouchard
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Mathieu Blanchette
- School of Computer Science , McGill University , 3480 University Street , Montréal , Quebec H3A 0E9 , Canada
| | - Marie-Soleil Gauthier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de Médecine , Université de Montréal , 2900 Boulevard Édouart-Montpetit , Montréal , Quebec H3T 1J4 , Canada
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32
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Morris DL, Kastner DW, Johnson S, Strub MP, He Y, Bleck CKE, Lee DY, Tjandra N. Humanin induces conformational changes in the apoptosis regulator BAX and sequesters it into fibers, preventing mitochondrial outer-membrane permeabilization. J Biol Chem 2019; 294:19055-19065. [PMID: 31690630 DOI: 10.1074/jbc.ra119.011297] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Indexed: 01/27/2023] Open
Abstract
The mitochondrial, or intrinsic, apoptosis pathway is regulated mainly by members of the B-cell lymphoma 2 (BCL-2) protein family. BCL-2-associated X apoptosis regulator (BAX) plays a pivotal role in the initiation of mitochondria-mediated apoptosis as one of the factors causing mitochondrial outer-membrane permeabilization (MOMP). Of current interest are endogenous BAX ligands that inhibit its MOMP activity. Mitochondrial-derived peptides (MDPs) are a recently identified class of mitochondrial retrograde signaling molecules and are reported to be potent apoptosis inhibitors. Among them, humanin (HN) has been shown to suppress apoptosis by inhibiting BAX translocation to the mitochondrial outer membrane, but the molecular mechanism of this interaction is unknown. Here, using recombinant protein expression, along with light-scattering, CD, and fluorescence spectroscopy, we report that HN and BAX can form fibers together in vitro Results from negative stain EM experiments suggest that BAX undergoes secondary and tertiary structural rearrangements and incorporates into the fibers, and that its membrane-associating C-terminal helix is important for the fibrillation process. Additionally, HN mutations known to alter its anti-apoptotic activity affect fiber morphology. Our findings reveal for the first time a potential mechanism by which BAX can be sequestered by fibril formation, which can prevent it from initiating MOMP and committing the cell to apoptosis.
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Affiliation(s)
- Daniel L Morris
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20814
| | - David W Kastner
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20814
| | - Sabrina Johnson
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20814
| | - Marie-Paule Strub
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20814.,Protein Expression Facility, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20814
| | - Yi He
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20814.,Protein Expression Facility, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20814
| | - Christopher K E Bleck
- Electron Microscopy Core Facility, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Duck-Yeon Lee
- Biochemistry Core Facility, NHLBI, National Institutes of Health, Bethesda, Maryland 20814
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20814
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33
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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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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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35
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36
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Identification of small ORF-encoded peptides in mouse serum. BIOPHYSICS REPORTS 2018; 4:39-49. [PMID: 29577068 PMCID: PMC5860097 DOI: 10.1007/s41048-018-0048-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/05/2017] [Indexed: 01/26/2023] Open
Abstract
Identification of the coding elements in the genome is fundamental to interpret the development of living systems and species diversity. Small peptides (length < 100 amino acids) have played an important role in regulating the biological metabolism, but their identification has been limited by their size and abundance. Serum is the most important body fluid and is full of small peptides. In this study, we have established a small ORF-encoded peptides (SEPs) database from mouse GENCODE release. This database provides about half a million putative translated SEPs in mouse. We also extract serum proteins from wild type and ob/ob mice, and collect the low molecular weight proteins for mass spectrometric analysis. More than 50 novel SEPs have been discovered. Several SEPs are further verified by biochemical method with newly raised antibodies. These novel SEPs enhance the knowledge about the complexity of serum and provide new clues for the annotation and functional analysis of genes, especially the noncoding elements in the genome.
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37
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Rytömaa T, Grip-Rytömaa K. Spontaneous death of rat chloroleukaemia cells induced by an endogenous growth inhibitor. Cell Prolif 2018; 51. [PMID: 29226462 PMCID: PMC6528872 DOI: 10.1111/cpr.12421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/28/2017] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVES When rat chloroleukaemia (CHL) cells are grown undisturbed in a confined space, a genomic long interspersed nuclear element (LINE) is transcriptionally activated at a relatively low population density, followed by the retrotransposition of LINE and population death. This death programme is fundamentally different from conventional cell death pathways. MATERIALS AND METHODS This work is essentially based on the re-analysis of relevant, old experimental data. Elemental analysis of a highly purified, long-stored inhibitor sample was performed. Genomic sequence searches were performed using the basic local alignment search tool (BLAST). RESULTS This death programme is initiated by an endogenous inhibitor secreted by CHL cells. The inhibitor is almost certainly identical to the pentapeptide pyroGlu-Glu-Asp-Cys-Lys, shown to be a cell line-specific inhibitor of normal granulocytic cells. The inhibitor is derived from a highly conserved short open reading frame in mammalian genomes. CONCLUSIONS Although spontaneous population death may be a biological oddity restricted to rat CHL cells, we suggest that this death programme is responsible for the eradication of cancer cells following treatment with an inhibitor administered exogenously.
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Affiliation(s)
- T Rytömaa
- Finnish Medical Society Duodecim, Helsinki, Finland
- Finnish Society of Radiobiology, Helsinki, Finland
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38
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He Y, Yuan C, Chen L, Lei M, Zellmer L, Huang H, Liao DJ. Transcriptional-Readthrough RNAs Reflect the Phenomenon of "A Gene Contains Gene(s)" or "Gene(s) within a Gene" in the Human Genome, and Thus Are Not Chimeric RNAs. Genes (Basel) 2018; 9:E40. [PMID: 29337901 PMCID: PMC5793191 DOI: 10.3390/genes9010040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/29/2017] [Accepted: 01/07/2018] [Indexed: 02/06/2023] Open
Abstract
Tens of thousands of chimeric RNAs, i.e., RNAs with sequences of two genes, have been identified in human cells. Most of them are formed by two neighboring genes on the same chromosome and are considered to be derived via transcriptional readthrough, but a true readthrough event still awaits more evidence and trans-splicing that joins two transcripts together remains as a possible mechanism. We regard those genomic loci that are transcriptionally read through as unannotated genes, because their transcriptional and posttranscriptional regulations are the same as those of already-annotated genes, including fusion genes formed due to genetic alterations. Therefore, readthrough RNAs and fusion-gene-derived RNAs are not chimeras. Only those two-gene RNAs formed at the RNA level, likely via trans-splicing, without corresponding genes as genomic parents, should be regarded as authentic chimeric RNAs. However, since in human cells, procedural and mechanistic details of trans-splicing have never been disclosed, we doubt the existence of trans-splicing. Therefore, there are probably no authentic chimeras in humans, after readthrough and fusion-gene derived RNAs are all put back into the group of ordinary RNAs. Therefore, it should be further determined whether in human cells all two-neighboring-gene RNAs are derived from transcriptional readthrough and whether trans-splicing truly exists.
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Affiliation(s)
- Yan He
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang City 443002, Hubei, China.
| | - Lichan Chen
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
| | - Mingjuan Lei
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
| | - Lucas Zellmer
- Masonic Cancer Center, University of Minnesota, 435 E. River Road, Minneapolis, MN 55455, USA.
| | - Hai Huang
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Dezhong Joshua Liao
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou, China.
- Department of Pathology, Guizhou Medical University Hospital, Guiyang 550004, Guizhou, China.
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39
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Olexiouk V, Van Criekinge W, Menschaert G. An update on sORFs.org: a repository of small ORFs identified by ribosome profiling. Nucleic Acids Res 2018; 46:D497-D502. [PMID: 29140531 PMCID: PMC5753181 DOI: 10.1093/nar/gkx1130] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022] Open
Abstract
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs. Furthermore, a novel noise filtering algorithm was designed, able to distinguish sORFs with true ribosomal activity from simulated noise, consequently reducing the false positive identification rate. The inclusion of other species also led to the development of an inner BLAST pipeline, assessing sequence similarity between sORFs in the repository. Building on the proof of concept model in the initial release of sORFs.org, a full PRIDE-ReSpin pipeline was now released, reprocessing publicly available MS-based proteomics PRIDE datasets, reporting on true translation events. Next to reporting those identified peptides, sORFs.org allows visual inspection of the annotated spectra within the Lorikeet MS/MS viewer, thus enabling detailed manual inspection and interpretation.
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Affiliation(s)
- Volodimir Olexiouk
- Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Wim Van Criekinge
- Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
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40
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Abstract
Koppel & Fainzilber review translatomics and proteomics methods for studying protein synthesis at subcellular resolution.
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Affiliation(s)
- Indrek Koppel
- Department of Biomolecular Sciences
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
| | - Mike Fainzilber
- Department of Biomolecular Sciences
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
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41
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Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci U S A 2017; 114:E10018-E10027. [PMID: 29087317 PMCID: PMC5699049 DOI: 10.1073/pnas.1708433114] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Noncoding RNAs are an underexplored reservoir of regulatory molecules in eukaryotes. We analyzed the environmental response of roots to phosphorus (Pi) nutrition to understand how a change in availability of an essential element is managed. Pi availability influenced translational regulation mediated by small upstream ORFs on protein-coding mRNAs. Discovery, classification, and evaluation of long noncoding RNAs (lncRNAs) associated with translating ribosomes uncovered diverse new examples of translational regulation. These included Pi-regulated small peptide synthesis, ribosome-coupled phased small interfering RNA production, and the translational regulation of natural antisense RNAs and other regulatory RNAs. This study demonstrates that translational control contributes to the stability and activity of regulatory RNAs, providing an avenue for manipulation of traits. Eukaryotic transcriptomes contain a major non–protein-coding component that includes precursors of small RNAs as well as long noncoding RNA (lncRNAs). Here, we utilized the mapping of ribosome footprints on RNAs to explore translational regulation of coding and noncoding RNAs in roots of Arabidopsis thaliana shifted from replete to deficient phosphorous (Pi) nutrition. Homodirectional changes in steady-state mRNA abundance and translation were observed for all but 265 annotated protein-coding genes. Of the translationally regulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on the principal protein-coding region. Nearly one-half of the 2,382 lncRNAs detected had ribosome footprints, including 56 with significantly altered translation under Pi-limited nutrition. The prediction of translated small ORFs (sORFs) by quantitation of translation termination and peptidic analysis identified lncRNAs that produce peptides, including several deeply evolutionarily conserved and significantly Pi-regulated lncRNAs. Furthermore, we discovered that natural antisense transcripts (NATs) frequently have actively translated sORFs, including five with low-Pi up-regulation that correlated with enhanced translation of the sense protein-coding mRNA. The data also confirmed translation of miRNA target mimics and lncRNAs that produce trans-acting or phased small-interfering RNA (tasiRNA/phasiRNAs). Mutational analyses of the positionally conserved sORF of TAS3a linked its translation with tasiRNA biogenesis. Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that nutrient availability and translational regulation controls protein and small peptide-encoding mRNAs as well as a diverse cadre of regulatory RNAs.
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42
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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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43
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Henninot A, Collins JC, Nuss JM. The Current State of Peptide Drug Discovery: Back to the Future? J Med Chem 2017; 61:1382-1414. [PMID: 28737935 DOI: 10.1021/acs.jmedchem.7b00318] [Citation(s) in RCA: 657] [Impact Index Per Article: 93.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, peptide drug discovery has experienced a revival of interest and scientific momentum, as the pharmaceutical industry has come to appreciate the role that peptide therapeutics can play in addressing unmet medical needs and how this class of compounds can be an excellent complement or even preferable alternative to small molecule and biological therapeutics. In this Perspective, we give a concise description of the recent progress in peptide drug discovery in a holistic manner, highlighting enabling technological advances affecting nearly every aspect of this field: from lead discovery, to synthesis and optimization, to peptide drug delivery. An emphasis is placed on describing research efforts to overcome the inherent weaknesses of peptide drugs, in particular their poor pharmacokinetic properties, and how these efforts have been critical to the discovery, design, and subsequent development of novel therapeutics.
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Affiliation(s)
- Antoine Henninot
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - James C Collins
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - John M Nuss
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
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44
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Gubala A, Walsh S, McAllister J, Weir R, Davis S, Melville L, Mitchell I, Bulach D, Gauci P, Skvortsov A, Boyle D. Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae. Evol Bioinform Online 2017; 13:1176934317713484. [PMID: 28747815 PMCID: PMC5510769 DOI: 10.1177/1176934317713484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/05/2017] [Indexed: 12/11/2022] Open
Abstract
Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.
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Affiliation(s)
- Aneta Gubala
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Susan Walsh
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Jane McAllister
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Richard Weir
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Steven Davis
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Lorna Melville
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Ian Mitchell
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Dieter Bulach
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
| | - Penny Gauci
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Alex Skvortsov
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - David Boyle
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
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45
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Chu Q, Rathore A, Diedrich JK, Donaldson CJ, Yates JR, Saghatelian A. Identification of Microprotein-Protein Interactions via APEX Tagging. Biochemistry 2017; 56:3299-3306. [PMID: 28589727 PMCID: PMC5499098 DOI: 10.1021/acs.biochem.7b00265] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/17/2017] [Indexed: 02/08/2023]
Abstract
Microproteins are peptides and small proteins encoded by small open reading frames (smORFs). Newer technologies have led to the recent discovery of hundreds to thousands of new microproteins. The biological functions of a few microproteins have been elucidated, and these microproteins have fundamental roles in biology ranging from limb development to muscle function, highlighting the value of characterizing these molecules. The identification of microprotein-protein interactions (MPIs) has proven to be a successful approach to the functional characterization of these genes; however, traditional immunoprecipitation methods result in the enrichment of nonspecific interactions for microproteins. Here, we test and apply an in situ proximity tagging method that relies on an engineered ascorbate peroxidase 2 (APEX) to elucidate MPIs. The results demonstrate that APEX tagging is superior to traditional immunoprecipitation methods for microproteins. Furthermore, the application of APEX tagging to an uncharacterized microprotein called C11orf98 revealed that this microprotein interacts with nucleolar proteins nucleophosmin and nucleolin, demonstrating the ability of this approach to identify novel hypothesis-generating MPIs.
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Affiliation(s)
- Qian Chu
- Clayton
Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Annie Rathore
- Clayton
Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
- Division
of Biological Sciences, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Jolene K. Diedrich
- Clayton
Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Cynthia J. Donaldson
- Clayton
Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - John R. Yates
- Department
of Chemical Physiology, The Scripps Research
Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Saghatelian
- Clayton
Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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46
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Zhu Y, Hassan YI, Lepp D, Shao S, Zhou T. Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins. Toxins (Basel) 2017; 9:E130. [PMID: 28387743 PMCID: PMC5408204 DOI: 10.3390/toxins9040130] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 02/01/2023] Open
Abstract
Mycotoxins, the secondary metabolites of mycotoxigenic fungi, have been found in almost all agricultural commodities worldwide, causing enormous economic losses in livestock production and severe human health problems. Compared to traditional physical adsorption and chemical reactions, interest in biological detoxification methods that are environmentally sound, safe and highly efficient has seen a significant increase in recent years. However, researchers in this field have been facing tremendous unexpected challenges and are eager to find solutions. This review summarizes and assesses the research strategies and methodologies in each phase of the development of microbiological solutions for mycotoxin mitigation. These include screening of functional microbial consortia from natural samples, isolation and identification of single colonies with biotransformation activity, investigation of the physiological characteristics of isolated strains, identification and assessment of the toxicities of biotransformation products, purification of functional enzymes and the application of mycotoxin decontamination to feed/food production. A full understanding and appropriate application of this tool box should be helpful towards the development of novel microbiological solutions on mycotoxin detoxification.
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Affiliation(s)
- Yan Zhu
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
| | - Yousef I Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
| | - Dion Lepp
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
| | - Suqin Shao
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
| | - Ting Zhou
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
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47
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Osbak KK, Houston S, Lithgow KV, Meehan CJ, Strouhal M, Šmajs D, Cameron CE, Van Ostade X, Kenyon CR, Van Raemdonck GA. Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry. PLoS Negl Trop Dis 2016; 10:e0004988. [PMID: 27606673 PMCID: PMC5015957 DOI: 10.1371/journal.pntd.0004988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/19/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection. METHODOLOGY/PRINCIPAL FINDINGS To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance. CONCLUSIONS This is the most comprehensive description of the global T. pallidum proteome to date. These data provide valuable insights into in vivo T. pallidum protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.
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Affiliation(s)
- Kara K Osbak
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Karen V Lithgow
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Conor J Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Xaveer Van Ostade
- Laboratory for Protein Science, Proteomics and Epigenetic Signaling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, Belgium
| | - Chris R Kenyon
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
| | - Geert A Van Raemdonck
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory for Protein Science, Proteomics and Epigenetic Signaling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, Belgium
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48
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Li H, Hu C, Bai L, Li H, Li M, Zhao X, Czajkowsky DM, Shao Z. Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryos reveals hundreds of conserved translated sORFs. DNA Res 2016; 23:571-580. [PMID: 27559081 PMCID: PMC5144680 DOI: 10.1093/dnares/dsw040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022] Open
Abstract
There is growing recognition that small open reading frames (sORFs) encoding peptides shorter than 100 amino acids are an important class of functional elements in the eukaryotic genome, with several already identified to play critical roles in growth, development, and disease. However, our understanding of their biological importance has been hindered owing to the significant technical challenges limiting their annotation. Here we combined ultra-deep sequencing of ribosome-associated poly-adenylated RNAs with rigorous conservation analysis to identify a comprehensive population of translated sORFs during early Drosophila embryogenesis. In total, we identify 399 sORFs, including those previously annotated but without evidence of translational capacity, those found within transcripts previously classified as non-coding, and those not previously known to be transcribed. Further, we find, for the first time, evidence for translation of many sORFs with different isoforms, suggesting their regulation is as complex as longer ORFs. Furthermore, many sORFs are found not associated with ribosomes in late-stage Drosophila S2 cells, suggesting that many of the translated sORFs may have stage-specific functions during embryogenesis. These results thus provide the first comprehensive annotation of the sORFs present during early Drosophila embryogenesis, a necessary basis for a detailed delineation of their function in embryogenesis and other biological processes.
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Affiliation(s)
- Hongmei Li
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ling Bai
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingfa Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Zhao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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49
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Redefining the Translational Status of 80S Monosomes. Cell 2016; 164:757-69. [PMID: 26871635 DOI: 10.1016/j.cell.2016.01.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/20/2015] [Accepted: 12/23/2015] [Indexed: 11/20/2022]
Abstract
Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remain controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ∼ 590 nt, and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs.
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50
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Servín-Blanco R, Zamora-Alvarado R, Gevorkian G, Manoutcharian K. Antigenic variability: Obstacles on the road to vaccines against traditionally difficult targets. Hum Vaccin Immunother 2016; 12:2640-2648. [PMID: 27295540 DOI: 10.1080/21645515.2016.1191718] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Despite the impressive impact of vaccines on public health, the success of vaccines targeting many important pathogens and cancers has to date been limited. The burden of infectious diseases today is mainly caused by antigenically variable pathogens (AVPs), which escape immune responses induced by prior infection or vaccination through changes in molecular structures recognized by antibodies or T cells. Extensive genetic and antigenic variability is the major obstacle for the development of new or improved vaccines against "difficult" targets. Alternative, qualitatively new approaches leading to the generation of disease- and patient-specific vaccine immunogens that incorporate complex permanently changing epitope landscapes of intended targets accompanied by appropriate immunomodulators are urgently needed. In this review, we highlight some of the most critical common issues related to the development of vaccines against many pathogens and cancers that escape protective immune responses owing to antigenic variation, and discuss recent efforts to overcome the obstacles by applying alternative approaches for the rational design of new types of immunogens.
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Affiliation(s)
- R Servín-Blanco
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - R Zamora-Alvarado
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - G Gevorkian
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
| | - K Manoutcharian
- a Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Cuidad Universitaria , México DF , México
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