1
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Yakubu B, Appiah EM, Adu AF. Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes. Int J Genomics 2024; 2024:5536117. [PMID: 38469580 PMCID: PMC10927345 DOI: 10.1155/2024/5536117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/20/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). Conclusion. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium's antibiotic resistance.
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Affiliation(s)
- Biigba Yakubu
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Edwin Moses Appiah
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Andrews Frimpong Adu
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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2
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Gallois M, Menoret D, Marques-Prieto S, Montigny A, Valenti P, Moussian B, Plaza S, Payre F, Chanut-Delalande H. Pri peptides temporally coordinate transcriptional programs during epidermal differentiation. SCIENCE ADVANCES 2024; 10:eadg8816. [PMID: 38335295 PMCID: PMC10857433 DOI: 10.1126/sciadv.adg8816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
To achieve a highly differentiated state, cells undergo multiple transcriptional processes whose coordination and timing are not well understood. In Drosophila embryonic epidermal cells, polished-rice (Pri) smORF peptides act as temporal mediators of ecdysone to activate a transcriptional program leading to cell shape remodeling. Here, we show that the ecdysone/Pri axis concomitantly represses the transcription of a large subset of cuticle genes to ensure proper differentiation of the insect exoskeleton. The repression relies on the transcription factor Ken and persists for several days throughout early larval stages, during which a soft cuticle allows larval crawling. The onset of these cuticle genes normally awaits the end of larval stages when the rigid pupal case assembles, and their premature expression triggers abnormal sclerotization of the larval cuticle. These results uncovered a temporal switch to set up distinct structures of cuticles adapted to the animal lifestyle and which might be involved in the evolutionary history of insects.
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Affiliation(s)
- Maylis Gallois
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Delphine Menoret
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Simon Marques-Prieto
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Audrey Montigny
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Philippe Valenti
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Bernard Moussian
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, CNRS/UPS/INPT, Auzeville-Tolosane, France
| | - François Payre
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Hélène Chanut-Delalande
- Molecular Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
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3
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Mohsen JJ, Martel AA, Slavoff SA. Microproteins-Discovery, structure, and function. Proteomics 2023; 23:e2100211. [PMID: 37603371 PMCID: PMC10841188 DOI: 10.1002/pmic.202100211] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Advances in proteogenomic technologies have revealed hundreds to thousands of translated small open reading frames (sORFs) that encode microproteins in genomes across evolutionary space. While many microproteins have now been shown to play critical roles in biology and human disease, a majority of recently identified microproteins have little or no experimental evidence regarding their functionality. Computational tools have some limitations for analysis of short, poorly conserved microprotein sequences, so additional approaches are needed to determine the role of each member of this recently discovered polypeptide class. A currently underexplored avenue in the study of microproteins is structure prediction and determination, which delivers a depth of functional information. In this review, we provide a brief overview of microprotein discovery methods, then examine examples of microprotein structures (and, conversely, intrinsic disorder) that have been experimentally determined using crystallography, cryo-electron microscopy, and NMR, which provide insight into their molecular functions and mechanisms. Additionally, we discuss examples of predicted microprotein structures that have provided insight or context regarding their function. Analysis of microprotein structure at the angstrom level, and confirmation of predicted structures, therefore, has potential to identify translated microproteins that are of biological importance and to provide molecular mechanism for their in vivo roles.
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Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alina A. Martel
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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4
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Klapproth C, Zötzsche S, Kühnl F, Fallmann J, Stadler P, Findeiß S. Tailored machine learning models for functional RNA detection in genome-wide screens. NAR Genom Bioinform 2023; 5:lqad072. [PMID: 37608800 PMCID: PMC10440787 DOI: 10.1093/nargab/lqad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/28/2023] [Accepted: 07/30/2023] [Indexed: 08/24/2023] Open
Abstract
The in silico prediction of non-coding and protein-coding genetic loci has received considerable attention in comparative genomics aiming in particular at the identification of properties of nucleotide sequences that are informative of their biological role in the cell. We present here a software framework for the alignment-based training, evaluation and application of machine learning models with user-defined parameters. Instead of focusing on the one-size-fits-all approach of pervasive in silico annotation pipelines, we offer a framework for the structured generation and evaluation of models based on arbitrary features and input data, focusing on stable and explainable results. Furthermore, we showcase the usage of our software package in a full-genome screen of Drosophila melanogaster and evaluate our results against the well-known but much less flexible program RNAz.
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Affiliation(s)
- Christopher Klapproth
- Leipzig University, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Bioinformatics Group, Härtelstrasse 16-18, D-04107 Leipzig, Germany
- ScaDS.AI Leipzig (Center for Scalable Data Analytics and Artificial Intelligence), Humboldtstraße 25, D-04105 Leipzig, Germany
| | - Siegfried Zötzsche
- Leipzig University, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Bioinformatics Group, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Felix Kühnl
- Leipzig University, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Bioinformatics Group, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Jörg Fallmann
- Leipzig University, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Bioinformatics Group, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Leipzig University, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Bioinformatics Group, Härtelstrasse 16-18, D-04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Science, Inselstraße 22, D-04103 Leipzig, Germany
- University of Vienna, Institute for Theoretical Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe NM 97501, USA
- Universidad Nacional de Colombia, Facultad de Ciencias, Bogotá, D.C., Colombia
| | - Sven Findeiß
- Leipzig University, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Bioinformatics Group, Härtelstrasse 16-18, D-04107 Leipzig, Germany
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5
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Huo LJ, Lu PY, Li DX, Shi XZ. The sORF-Encoded Peptides, ATP Synthase Subunits, Facilitate WSSV Duplication in Shrimp. Viruses 2022; 14:2449. [PMID: 36366547 PMCID: PMC9692589 DOI: 10.3390/v14112449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
Abstract
Short open reading frames (sORFs) are a newly identified family of genes, and the functions of most sORF genes and their encoded peptides (SEPs) are still unknown. In this study, two ATP synthase subunits were identified in kuruma shrimp (Marsupenaeus japonicus) as SEPs, namely MjATP5I and MjATP5L. They were widely distributed in all of the tested tissues of shrimp and upregulated in hemocytes and intestines in response to WSSV challenge. The injection of recombinant proteins (rMjATP5I and rMjATP5L) increased the expression of Ie1 and Vp28, while the knockdown of MjATP5I and MjATP5L decreased the expression of Ie1 and Vp28. All of the results suggest that MjATP5I and MjATP5L were beneficial for WSSV replication. Further exploration found that MjATP5I and MjATP5L RNAi significantly improved the shrimp survival rates, reduced ATP production, and upregulated the expression of antimicrobial peptide genes post viral challenge, and the two ATPase subunits and Relish negatively regulated each other. These results reveal that MjATP5I and MjATP5L facilitated WSSV duplication by regulating the production of ATP contents and the expression of antimicrobial peptide genes in shrimp.
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Affiliation(s)
- Li-Jie Huo
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Peng-Yuan Lu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Dian-Xiang Li
- Department of Biopharmacy, School of Biological Sciences and Biotechnology, University of Jinan, Jinan 250022, China
| | - Xiu-Zhen Shi
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
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6
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Fu H, Wang T, Kong X, Yan K, Yang Y, Cao J, Yuan Y, Wang N, Kee K, Lu ZJ, Xi Q. A Nodal enhanced micropeptide NEMEP regulates glucose uptake during mesendoderm differentiation of embryonic stem cells. Nat Commun 2022; 13:3984. [PMID: 35810171 PMCID: PMC9271079 DOI: 10.1038/s41467-022-31762-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
TGF-β family proteins including Nodal are known as central regulators of early development in metazoans, yet our understanding of the scope of Nodal signaling’s downstream targets and associated physiological mechanisms in specifying developmentally appropriate cell fates is far from complete. Here, we identified a highly conserved, transmembrane micropeptide—NEMEP—as a direct target of Nodal signaling in mesendoderm differentiation of mouse embryonic stem cells (mESCs), and this micropeptide is essential for mesendoderm differentiation. We showed that NEMEP interacts with the glucose transporters GLUT1/GLUT3 and promotes glucose uptake likely through these interactions. Thus, beyond expanding the scope of known Nodal signaling targets in early development and showing that this target micropeptide augments the glucose uptake during mesendoderm differentiation, our study provides a clear example for the direct functional impact of altered glucose metabolism on cell fate determination. Fu et al. identify the highly conserved, transmembrane micropeptide, NEMEP, as a direct target of Nodal signaling, essential for mesendoderm differentiation. NEMEP interacts with the glucose transporters GLUT1/GLUT3 and promotes glucose uptake.
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Affiliation(s)
- Haipeng Fu
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tingyu Wang
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaohui Kong
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kun Yan
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yang Yang
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-NIBS, Tsinghua University, Beijing, 100084, China
| | - Jingyi Cao
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yafei Yuan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Nan Wang
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Kehkooi Kee
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zhi John Lu
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Joint Graduate Program of Peking-Tsinghua-NIBS, Tsinghua University, Beijing, 100084, China.
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7
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Zhang Z, Li Y, Yuan W, Wang Z, Wan C. Proteomic-driven identification of short open reading frame-encoded peptides. Proteomics 2022; 22:e2100312. [PMID: 35384297 DOI: 10.1002/pmic.202100312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022]
Abstract
Accumulating evidence has shown that a large number of short open reading frames (sORFs) also have the ability to encode proteins. The discovery of sORFs opens up a new research area, leading to the identification and functional study of sORF encoded peptides (SEPs) at the omics level. Besides bioinformatics prediction and ribosomal profiling, mass spectrometry (MS) has become a significant tool as it directly detects the sequence of SEPs. Though MS-based proteomics methods have proved to be effective for qualitative and quantitative analysis of SEPs, the detection of SEPs is still a great challenge due to their low abundance and short sequence. To illustrate the progress in method development, we described and discussed the main steps of large-scale proteomics identification of SEPs, including SEP extraction and enrichment, MS detection, data processing and quality control, quantification, and function prediction and validation methods. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zheng Zhang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Yujie Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Wenqian Yuan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Zhiwei Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
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8
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Lee J, Wacholder A, Carvunis AR. Evolutionary Characterization of the Short Protein SPAAR. Genes (Basel) 2021; 12:genes12121864. [PMID: 34946813 PMCID: PMC8702040 DOI: 10.3390/genes12121864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
Microproteins (<100 amino acids) are receiving increasing recognition as important participants in numerous biological processes, but their evolutionary dynamics are poorly understood. SPAAR is a recently discovered microprotein that regulates muscle regeneration and angiogenesis through interactions with conserved signaling pathways. Interestingly, SPAAR does not belong to any known protein family and has known homologs exclusively among placental mammals. This lack of distant homology could be caused by challenges in homology detection of short sequences, or it could indicate a recent de novo emergence from a noncoding sequence. By integrating syntenic alignments and homology searches, we identify SPAAR orthologs in marsupials and monotremes, establishing that SPAAR has existed at least since the emergence of mammals. SPAAR shows substantial primary sequence divergence but retains a conserved protein structure. In primates, we infer two independent evolutionary events leading to the de novo origination of 5' elongated isoforms of SPAAR from a noncoding sequence and find evidence of adaptive evolution in this extended region. Thus, SPAAR may be of ancient origin, but it appears to be experiencing continual evolutionary innovation in mammals.
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Affiliation(s)
- Jiwon Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; (J.L.); (A.W.)
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; (J.L.); (A.W.)
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; (J.L.); (A.W.)
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Correspondence: ; Tel.: +1-412-648-3335
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9
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Dib A, Zanet J, Mancheno-Ferris A, Gallois M, Markus D, Valenti P, Marques-Prieto S, Plaza S, Kageyama Y, Chanut-Delalande H, Payre F. Pri smORF Peptides Are Wide Mediators of Ecdysone Signaling, Contributing to Shape Spatiotemporal Responses. Front Genet 2021; 12:714152. [PMID: 34527021 DOI: 10.3389/fgene.2021.714152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
There is growing evidence that peptides encoded by small open-reading frames (sORF or smORF) can fulfill various cellular functions and define a novel class regulatory molecules. To which extend transcripts encoding only smORF peptides compare with canonical protein-coding genes, yet remain poorly understood. In particular, little is known on whether and how smORF-encoding RNAs might need tightly regulated expression within a given tissue, at a given time during development. We addressed these questions through the analysis of Drosophila polished rice (pri, a.k.a. tarsal less or mille pattes), which encodes four smORF peptides (11-32 amino acids in length) required at several stages of development. Previous work has shown that the expression of pri during epidermal development is regulated in the response to ecdysone, the major steroid hormone in insects. Here, we show that pri transcription is strongly upregulated by ecdysone across a large panel of cell types, suggesting that pri is a core component of ecdysone response. Although pri is produced as an intron-less short transcript (1.5 kb), genetic assays reveal that the developmental functions of pri require an unexpectedly large array of enhancers (spanning over 50 kb), driving a variety of spatiotemporal patterns of pri expression across developing tissues. Furthermore, we found that separate pri enhancers are directly activated by the ecdysone nuclear receptor (EcR) and display distinct regulatory modes between developmental tissues and/or stages. Alike major developmental genes, the expression of pri in a given tissue often involves several enhancers driving apparently redundant (or shadow) expression, while individual pri enhancers can harbor pleiotropic functions across tissues. Taken together, these data reveal the broad role of Pri smORF peptides in ecdysone signaling and show that the cis-regulatory architecture of the pri gene contributes to shape distinct spatial and temporal patterns of ecdysone response throughout development.
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Affiliation(s)
- Azza Dib
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Jennifer Zanet
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Alexandra Mancheno-Ferris
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Maylis Gallois
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Damien Markus
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Philippe Valenti
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Simon Marques-Prieto
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Serge Plaza
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Yuji Kageyama
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan.,Biosignal Research Center, Kobe University, Kobe, Japan
| | - Hélène Chanut-Delalande
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - François Payre
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
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10
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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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11
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Choteau SA, Wagner A, Pierre P, Spinelli L, Brun C. MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6307706. [PMID: 34156446 PMCID: PMC8218702 DOI: 10.1093/database/baab032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/08/2021] [Accepted: 05/17/2021] [Indexed: 11/12/2022]
Abstract
The development of high-throughput technologies revealed the existence of non-canonical short open reading frames (sORFs) on most eukaryotic ribonucleic acids. They are ubiquitous genetic elements conserved across species and suspected to be involved in numerous cellular processes. MetamORF (https://metamorf.hb.univ-amu.fr/) aims to provide a repository of unique sORFs identified in the human and mouse genomes with both experimental and computational approaches. By gathering publicly available sORF data, normalizing them and summarizing redundant information, we were able to identify a total of 1 162 675 unique sORFs. Despite the usual characterization of ORFs as short, upstream or downstream, there is currently no clear consensus regarding the definition of these categories. Thus, the data have been reprocessed using a normalized nomenclature. MetamORF enables new analyses at locus, gene, transcript and ORF levels, which should offer the possibility to address new questions regarding sORF functions in the future. The repository is available through an user-friendly web interface, allowing easy browsing, visualization, filtering over multiple criteria and export possibilities. sORFs can be searched starting from a gene, a transcript and an ORF ID, looking in a genome area or browsing the whole repository for a species. The database content has also been made available through track hubs at UCSC Genome Browser. Finally, we demonstrated an enrichment of genes harboring upstream ORFs among genes expressed in response to reticular stress. Database URL https://metamorf.hb.univ-amu.fr/.
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Affiliation(s)
- Sebastien A Choteau
- Aix-Marseille University, INSERM, TAGC, Turing Centre for Living Systems, 163 Avenue de Luminy, Marseille 13009, France.,Aix-Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, 163 Avenue de Luminy, Marseille 13009, France
| | - Audrey Wagner
- Aix-Marseille University, INSERM, TAGC, Turing Centre for Living Systems, 163 Avenue de Luminy, Marseille 13009, France
| | - Philippe Pierre
- Aix-Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, 163 Avenue de Luminy, Marseille 13009, France.,Department of Medical Sciences, Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, University of Aveiro, Aveiro 3810-193, Portugal.,Shanghai Institute of Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lionel Spinelli
- Aix-Marseille University, INSERM, TAGC, Turing Centre for Living Systems, 163 Avenue de Luminy, Marseille 13009, France.,Aix-Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, 163 Avenue de Luminy, Marseille 13009, France
| | - Christine Brun
- Aix-Marseille University, INSERM, TAGC, Turing Centre for Living Systems, 163 Avenue de Luminy, Marseille 13009, France.,CNRS, 31 Chemin Joseph Aiguier, Marseille 13009, France
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12
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Tharakan R, Sawa A. Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods. Front Genet 2021; 12:651485. [PMID: 34025718 PMCID: PMC8136307 DOI: 10.3389/fgene.2021.651485] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
A novel class of small proteins, called micropeptides, has recently been discovered in the genome. These proteins, which have been found to play important roles in many physiological and cellular systems, are shorter than 100 amino acids and were overlooked during previous genome annotations. Discovery and characterization of more micropeptides has been ongoing, often using -omics methods such as proteomics, RNA sequencing, and ribosome profiling. In this review, we survey the recent advances in the micropeptides field and describe the methodological and conceptual challenges facing future micropeptide endeavors.
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Affiliation(s)
- Ravi Tharakan
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Akira Sawa
- Departments of Psychiatry, Neuroscience, Biomedical Engineering, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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13
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Königsmann T, Parfentev I, Urlaub H, Riedel D, Schuh R. The bicistronic gene würmchen encodes two essential components for epithelial development in Drosophila. Dev Biol 2020; 463:53-62. [PMID: 32361005 DOI: 10.1016/j.ydbio.2020.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/17/2020] [Accepted: 04/07/2020] [Indexed: 11/24/2022]
Abstract
Epithelial tissues are fundamental for the establishment and maintenance of different body compartments in multicellular animals. To achieve this specific task epithelial sheets secrete an apical extracellular matrix for tissue strength and protection and they organize a transepithelial barrier function, which is mediated by tight junctions in vertebrates or septate junctions in invertebrates. Here, we show that the bicistronic gene würmchen is functionally expressed in epithelial tissues. CRISPR/Cas9-mediated mutations in both coding sequences reveal two essential polypeptides, Würmchen1 and Würmchen2, which are both necessary for normal epithelial tissue development. Würmchen1 represents a genuine septate junction core component. It is required during embryogenesis for septate junction organization, the establishment of a transepithelial barrier function, distinct cellular transport processes and tracheal system morphogenesis. Würmchen2 is localized in the apical membrane region of epithelial tissues and in a central core of the tracheal lumen during embryogenesis. It is essential during the later larval development.
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Affiliation(s)
- Tatiana Königsmann
- Research Group Molecular Organogenesis, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, D-37077, Göttingen, Germany
| | - Iwan Parfentev
- Research Group Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, D-37077, Göttingen, Germany
| | - Henning Urlaub
- Research Group Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, D-37077, Göttingen, Germany; Bioanalytics, Institute for Clinical Chemistry, University Medical Center, Robert-Koch-Strasse 420, 37075 Göttingen, Germany
| | - Dietmar Riedel
- Electron Microscopy Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, D-37077, Göttingen, Germany
| | - Reinhard Schuh
- Research Group Molecular Organogenesis, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, D-37077, Göttingen, Germany.
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14
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Tobias-Santos V, Guerra-Almeida D, Mury F, Ribeiro L, Berni M, Araujo H, Logullo C, Feitosa NM, de Souza-Menezes J, Pessoa Costa E, Nunes-da-Fonseca R. Multiple Roles of the Polycistronic Gene Tarsal-less/Mille-Pattes/Polished-Rice During Embryogenesis of the Kissing Bug Rhodnius prolixus. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Ray S, Rosenberg MI, Chanut-Delalande H, Decaras A, Schwertner B, Toubiana W, Auman T, Schnellhammer I, Teuscher M, Valenti P, Khila A, Klingler M, Payre F. The mlpt/Ubr3/Svb module comprises an ancient developmental switch for embryonic patterning. eLife 2019; 8:e39748. [PMID: 30896406 PMCID: PMC6428570 DOI: 10.7554/elife.39748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 03/07/2019] [Indexed: 12/30/2022] Open
Abstract
Small open reading frames (smORFs) encoding 'micropeptides' exhibit remarkable evolutionary complexity. Conserved peptides encoded by mille-pattes (mlpt)/polished rice (pri)/tarsal less (tal) are essential for embryo segmentation in Tribolium but, in Drosophila, function in terminal epidermal differentiation and patterning of adult legs. Here, we show that a molecular complex identified in Drosophila epidermal differentiation, comprising Mlpt peptides, ubiquitin-ligase Ubr3 and transcription factor Shavenbaby (Svb), represents an ancient developmental module required for early insect embryo patterning. We find that loss of segmentation function for this module in flies evolved concomitantly with restriction of Svb expression in early Drosophila embryos. Consistent with this observation, artificially restoring early Svb expression in flies causes segmentation defects that depend on mlpt function, demonstrating enduring potency of an ancestral developmental switch despite evolving embryonic patterning modes. These results highlight the evolutionary plasticity of conserved molecular complexes under the constraints of essential genetic networks. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Suparna Ray
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | - Miriam I Rosenberg
- Department of Ecology, Evolution and BehaviorHebrew University of JerusalemJerusalemIsrael
| | | | | | - Barbara Schwertner
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | | | - Tzach Auman
- Department of Ecology, Evolution and BehaviorHebrew University of JerusalemJerusalemIsrael
| | - Irene Schnellhammer
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | - Matthias Teuscher
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | - Philippe Valenti
- Centre de Biologie du Développement, Université Paul Sabatier de ToulouseToulouseFrance
| | | | - Martin Klingler
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | - François Payre
- Centre de Biologie du Développement, Université Paul Sabatier de ToulouseToulouseFrance
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16
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Schiemann R, Lammers K, Janz M, Lohmann J, Paululat A, Meyer H. Identification and In Vivo Characterisation of Cardioactive Peptides in Drosophila melanogaster. Int J Mol Sci 2018; 20:ijms20010002. [PMID: 30577424 PMCID: PMC6337577 DOI: 10.3390/ijms20010002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/22/2018] [Indexed: 12/23/2022] Open
Abstract
Neuropeptides and peptide hormones serve as critical regulators of numerous biological processes, including development, growth, reproduction, physiology, and behaviour. In mammals, peptidergic regulatory systems are complex and often involve multiple peptides that act at different levels and relay to different receptors. To improve the mechanistic understanding of such complex systems, invertebrate models in which evolutionarily conserved peptides and receptors regulate similar biological processes but in a less complex manner have emerged as highly valuable. Drosophila melanogaster represents a favoured model for the characterisation of novel peptidergic signalling events and for evaluating the relevance of those events in vivo. In the present study, we analysed a set of neuropeptides and peptide hormones for their ability to modulate cardiac function in semi-intact larval Drosophila melanogaster. We identified numerous peptides that significantly affected heart parameters such as heart rate, systolic and diastolic interval, rhythmicity, and contractility. Thus, peptidergic regulation of the Drosophila heart is not restricted to chronotropic adaptation but also includes inotropic modulation. By specifically interfering with the expression of corresponding peptides in transgenic animals, we assessed the in vivo relevance of the respective peptidergic regulation. Based on the functional conservation of certain peptides throughout the animal kingdom, the identified cardiomodulatory activities may be relevant not only to proper heart function in Drosophila, but also to corresponding processes in vertebrates, including humans.
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Affiliation(s)
- Ronja Schiemann
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Kay Lammers
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Maren Janz
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Jana Lohmann
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Achim Paululat
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Heiko Meyer
- Department of Zoology and Developmental Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
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17
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Bohère J, Mancheno-Ferris A, Al Hayek S, Zanet J, Valenti P, Akino K, Yamabe Y, Inagaki S, Chanut-Delalande H, Plaza S, Kageyama Y, Osman D, Polesello C, Payre F. Shavenbaby and Yorkie mediate Hippo signaling to protect adult stem cells from apoptosis. Nat Commun 2018; 9:5123. [PMID: 30504772 PMCID: PMC6269459 DOI: 10.1038/s41467-018-07569-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/12/2018] [Indexed: 01/06/2023] Open
Abstract
To compensate for accumulating damages and cell death, adult homeostasis (e.g., body fluids and secretion) requires organ regeneration, operated by long-lived stem cells. How stem cells can survive throughout the animal life remains poorly understood. Here we show that the transcription factor Shavenbaby (Svb, OvoL in vertebrates) is expressed in renal/nephric stem cells (RNSCs) of Drosophila and required for their maintenance during adulthood. As recently shown in embryos, Svb function in adult RNSCs further needs a post-translational processing mediated by the Polished rice (Pri) smORF peptides and impairing Svb function leads to RNSC apoptosis. We show that Svb interacts both genetically and physically with Yorkie (YAP/TAZ in vertebrates), a nuclear effector of the Hippo pathway, to activate the expression of the inhibitor of apoptosis DIAP1. These data therefore identify Svb as a nuclear effector in the Hippo pathway, critical for the survival of adult somatic stem cells.
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Affiliation(s)
- Jérôme Bohère
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Alexandra Mancheno-Ferris
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Sandy Al Hayek
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
- Faculty of Sciences III, Lebanese University, Tripoli, 1300, Lebanon
- Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300, Lebanon
| | - Jennifer Zanet
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Philippe Valenti
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Kohsuke Akino
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
| | - Yuya Yamabe
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
| | - Sachi Inagaki
- Biosignal Research Center, Kobe University, 1-1 Rokko-dai, Nada, Kobe, 657-8501, Japan
| | - Hélène Chanut-Delalande
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Serge Plaza
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
- Laboratoire de Recherche en Sciences Végétales (LSRV), CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, 31326, Castanet-Tolosan, France
| | - Yuji Kageyama
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
- Biosignal Research Center, Kobe University, 1-1 Rokko-dai, Nada, Kobe, 657-8501, Japan
| | - Dani Osman
- Faculty of Sciences III, Lebanese University, Tripoli, 1300, Lebanon
- Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300, Lebanon
| | - Cédric Polesello
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France.
| | - François Payre
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France.
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18
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Abstract
A large body of evidence indicates that genome annotation pipelines have biased our view of coding sequences because they generally undersample small proteins and peptides. The recent development of genome-wide translation profiling reveals the prevalence of small/short open reading frames (smORFs or sORFs), which are scattered over all classes of transcripts, including both mRNAs and presumptive long noncoding RNAs. Proteomic approaches further confirm an unexpected variety of smORF-encoded peptides (SEPs), representing an overlooked reservoir of bioactive molecules. Indeed, functional studies in a broad range of species from yeast to humans demonstrate that SEPs can harbor key activities for the control of development, differentiation, and physiology. Here we summarize recent advances in the discovery and functional characterization of smORF/SEPs and discuss why these small players can no longer be ignored with regard to genome function.
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Affiliation(s)
- Serge Plaza
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse, Université Paul Sabatier, 31326 Castanet Tolosan, France; .,CNRS, UMR5546, Laboratoire de Recherches en Sciences Végétales, 31326 Castanet Tolosan, France
| | - Gerben Menschaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, University of Ghent, 9000 Gent, Belgium
| | - François Payre
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier, 31062 Toulouse, France;
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19
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Lopez-Ezquerra A, Harrison MC, Bornberg-Bauer E. Comparative analysis of lincRNA in insect species. BMC Evol Biol 2017; 17:155. [PMID: 28673235 PMCID: PMC5494802 DOI: 10.1186/s12862-017-0985-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/02/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The ever increasing availability of genomes makes it possible to investigate and compare not only the genomic complements of genes and proteins, but also of RNAs. One class of RNAs, the long noncoding RNAs (lncRNAs) and, in particular, their subclass of long intergenic noncoding RNAs (lincRNAs) have recently gained much attention because of their roles in regulation of important biological processes such as immune response or cell differentiation and as possible evolutionary precursors for protein coding genes. lincRNAs seem to be poorly conserved at the sequence level but at least some lincRNAs have conserved structural elements and syntenic genomic positions. Previous studies showed that transposable elements are a main contribution to the evolution of lincRNAs in mammals. In contrast, plant lincRNA emergence and evolution has been linked with local duplication events. However, little is known about their evolutionary dynamics in general and in insect genomes in particular. RESULTS Here we compared lincRNAs between seven insect genomes and investigated possible evolutionary changes and functional roles. We find very low sequence conservation between different species and that similarities within a species are mostly due to their association with transposable elements (TE) and simple repeats. Furthermore, we find that TEs are less frequent in lincRNA exons than in their introns, indicating that TEs may have been removed by selection. When we analysed the predicted thermodynamic stabilities of lincRNAs we found that they are more stable than their randomized controls which might indicate some selection pressure to maintain certain structural elements. We list several of the most stable lincRNAs which could serve as prime candidates for future functional studies. We also discuss the possibility of de novo protein coding genes emerging from lincRNAs. This is because lincRNAs with high GC content and potentially with longer open reading frames (ORF) are candidate loci where de novo gene emergence might occur. CONCLUSION The processes responsible for the emergence and diversification of lincRNAs in insects remain unclear. Both duplication and transposable elements may be important for the creation of new lincRNAs in insects.
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Affiliation(s)
- Alberto Lopez-Ezquerra
- Institute of Evolution and Biodiversity, University of Münster, Hüfferstrasse,1, Münster, Münster, Germany
| | - Mark C Harrison
- Institute of Evolution and Biodiversity, University of Münster, Hüfferstrasse,1, Münster, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute of Evolution and Biodiversity, University of Münster, Hüfferstrasse,1, Münster, Münster, Germany.
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20
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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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