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Lughmani H, Patel H, Chakravarti R. Structural Features and Physiological Associations of Human 14-3-3ζ Pseudogenes. Genes (Basel) 2024; 15:399. [PMID: 38674334 PMCID: PMC11049341 DOI: 10.3390/genes15040399] [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: 03/05/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
There are about 14,000 pseudogenes that are mutated or truncated sequences resembling functional parent genes. About two-thirds of pseudogenes are processed, while others are duplicated. Although initially thought dead, emerging studies indicate they have functional and regulatory roles. We study 14-3-3ζ, an adaptor protein that regulates cytokine signaling and inflammatory diseases, including rheumatoid arthritis, cancer, and neurological disorders. To understand how 14-3-3ζ (gene symbol YWHAZ) performs diverse functions, we examined the human genome and identified nine YWHAZ pseudogenes spread across many chromosomes. Unlike the 32 kb exon-to-exon sequence in YWHAZ, all pseudogenes are much shorter and lack introns. Out of six, four YWHAZ exons are highly conserved, but the untranslated region (UTR) shows significant diversity. The putative amino acid sequence of pseudogenes is 78-97% homologous, resulting in striking structural similarities with the parent protein. The OMIM and Decipher database searches revealed chromosomal loci containing pseudogenes are associated with human diseases that overlap with the parent gene. To the best of our knowledge, this is the first report on pseudogenes of the 14-3-3 family protein and their implications for human health. This bioinformatics-based study introduces a new insight into the complexity of 14-3-3ζ's functions in biology.
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Affiliation(s)
| | | | - Ritu Chakravarti
- Department of Physiology and Pharmacology, The University of Toledo, Toledo, OH 43614, USA; (H.L.); (H.P.)
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2
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Pan C, Mao S, Xiong Z, Chen Z, Xu N. Glutamate dehydrogenase: Potential therapeutic targets for neurodegenerative disease. Eur J Pharmacol 2023; 950:175733. [PMID: 37116563 DOI: 10.1016/j.ejphar.2023.175733] [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: 09/24/2022] [Revised: 03/31/2023] [Accepted: 04/17/2023] [Indexed: 04/30/2023]
Abstract
Glutamate dehydrogenase (GDH) is a key enzyme in mammalian glutamate metabolism. It is located at the intersection of multiple metabolic pathways and participates in a variety of cellular activities. GDH activity is strictly regulated by a variety of allosteric compounds. Here, we review the unique distribution and expressions of GDH in the brain nervous system. GDH plays an essential role in the glutamate-glutamine-GABA cycle between astrocytes and neurons. The dysfunction of GDH may induce the occurrence of many neurodegenerative diseases, such as Parkinson's disease, epilepsy, Alzheimer's disease, schizophrenia, and frontotemporal dementia. GDH activators and gene therapy have been found to protect neurons and improve motor disorders in neurodegenerative diseases caused by glutamate metabolism disorders. To date, no medicine has been discovered that specifically targets neurodegenerative diseases, although several potential medicines are used clinically. Targeting GDH to treat neurodegenerative diseases is expected to provide new insights and treatment strategies.
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Affiliation(s)
- Chuqiao Pan
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, 313200, Zhejiang, People's Republic of China
| | - Shijie Mao
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, 313200, Zhejiang, People's Republic of China
| | - Zeping Xiong
- Department of Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Huzhou, 313200, Zhejiang, People's Republic of China
| | - Zhao Chen
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, 313200, Zhejiang, People's Republic of China
| | - Ning Xu
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, 313200, Zhejiang, People's Republic of China.
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3
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Elucidation of a complete mechanical signaling and virulence activation pathway in enterohemorrhagic Escherichia coli. Cell Rep 2022; 39:110614. [PMID: 35385749 DOI: 10.1016/j.celrep.2022.110614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 12/09/2021] [Accepted: 03/13/2022] [Indexed: 12/23/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important extracellular human pathogen. The initial adherence of EHEC to host cells is a major cue for transcriptional induction of the locus of enterocyte effacement (LEE) genes to promote colonization and pathogenesis, but the mechanism through which this adherence is sensed and the LEE is induced remains largely elusive. Here, we report a complete signal transduction pathway for this virulence activation process. In this pathway, the outer-membrane lipoprotein NlpE senses a mechanical cue generated from initial host adherence and activates the BaeSR two-component regulatory system; the response regulator BaeR then directly activates the expression of airA located on O-island-134 and encoding a LEE transcriptional activator. Disruption of this pathway severely attenuates EHEC O157:H7 virulence both in vitro and in vivo. This study provides further insights into the evolution of EHEC pathogenesis and the host-pathogen interaction.
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4
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Huang S, Liao Q, Li W, Deng G, Jia M, Fang Q, Ji H, Meng M. The lncRNA PTTG3P promotes the progression of CRPC via upregulating PTTG1. Bull Cancer 2021; 108:359-368. [PMID: 33743960 DOI: 10.1016/j.bulcan.2020.11.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 11/18/2022]
Abstract
BACKGROUND Overexpression of certain long non-coding RNAs (lncRNAs) promotes the progression of castration-resistant prostate cancer (CRPC). The significance and potential role of the lncRNA designated pituitary tumour-transforming 3, pseudogene (PTTG3P) in CRPC is unknown. METHODS We detected PTTG3P expression by qPCR. Upregulated PTTG3P expression was performed to explore the role of PTTG3P in PCa cells resistant to ADT (androgen deprivation therapy). The relationship among PTTG3P, mir-146a-3p and PTTG1 were validated by qPCR, western blot and luciferase assay. RESULTS PTTG3P levels were significantly increased in the androgen-independent PC cell lines, as well as in CRPC tissues compared with those of the androgen-dependent prostate cancer cell line LNCaP and tumour tissues of patients with hormone-naive prostate cancers. Enforced expression of PTTG3P in androgen-deprived LNCaP cells significantly enhanced survival, clonogenicity, and tumorigenicity. Further, PTTG3P acted as a competing endogenous RNA (ceRNA, natural miRNA sponge) to upregulate PTTG1 expression by competing for mir-146a-3p in the progression to CRPC. CONCLUSION Our findings suggest that PTTG3P promotes the resistance of prostate cancer cells to androgen-deprivation therapy via upregulating PTTG1. PTTG3P may therefore represent a potential target for therapy of CRPC.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Androgen Antagonists/therapeutic use
- Anilides/therapeutic use
- Animals
- Antineoplastic Agents, Hormonal/therapeutic use
- Binding, Competitive
- Cell Line, Tumor
- Drug Resistance, Neoplasm
- Heterografts
- Humans
- Male
- Mice, Nude
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplasm Transplantation
- Nitriles/therapeutic use
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/pathology
- Pseudogenes
- RNA, Long Noncoding/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Securin/biosynthesis
- Securin/genetics
- Tosyl Compounds/therapeutic use
- Tumor Stem Cell Assay
- Up-Regulation
- Mice
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Affiliation(s)
- Shengquan Huang
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Qianjin Liao
- Chongqing north KuanRen hospital, 400000 Chongqing, China
| | - Weibing Li
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Guoxian Deng
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Ming Jia
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Qiang Fang
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China
| | - Huixiang Ji
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China.
| | - Mingsen Meng
- Chongqing medical university, The third affiliated hospital (General Hospital), Department of urology, 401120 Chongqing, China.
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Zhou D, Ren K, Wang M, Wang J, Li E, Hou C, Su Y, Jin Y, Zou Q, Zhou P, Liu X. Long non-coding RNA RACGAP1P promotes breast cancer invasion and metastasis via miR-345-5p/RACGAP1-mediated mitochondrial fission. Mol Oncol 2020; 15:543-559. [PMID: 33252198 PMCID: PMC7858103 DOI: 10.1002/1878-0261.12866] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/25/2020] [Accepted: 11/27/2020] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as key molecules in various cancers, yet their potential roles in the pathogenesis of breast cancer are not fully understood. Herein, using microarray analysis, we revealed that the lncRNA RACGAP1P, the pseudogene of Rac GTPase activating protein 1 (RACGAP1), was up-regulated in breast cancer tissues. Its high expression was confirmed in 25 pairs of breast cancer tissues and 8 breast cell lines by qRT-PCR. Subsequently, we found that RACGAP1P expression was positively correlated with lymph node metastasis, distant metastasis, TNM stage, and shorter survival time in 102 breast cancer patients. Then, in vitro and in vivo experiments were designed to investigate the biological function and regulatory mechanism of RACGAP1P in breast cancer cell lines. Overexpression of RACGAP1P in MDA-MB-231 and MCF7 breast cell lines increased their invasive ability and enhanced their mitochondrial fission. Conversely, inhibition of mitochondrial fission by Mdivi-1 could reduce the invasive ability of RACGAP1P-overexpressing cell lines. Furthermore, the promotion of mitochondrial fission by RACGAP1P depended on its competitive binding with miR-345-5p against its parental gene RACGAP1, leading to the activation of dynamin-related protein 1 (Drp1). In conclusion, lncRNA RACGAP1P promotes breast cancer invasion and metastasis via miR-345-5p/RACGAP1 pathway-mediated mitochondrial fission.
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Affiliation(s)
- Danmei Zhou
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kehan Ren
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Meili Wang
- Department of Pathology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Jigang Wang
- Department of Pathology, The Affiliated Hospital of Qingdao University, China
| | - Ermin Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chenjian Hou
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ying Su
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yiting Jin
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiang Zou
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ping Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiuping Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Department of Pathology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
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6
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Molecular fossils “pseudogenes” as functional signature in biological system. Genes Genomics 2020; 42:619-630. [DOI: 10.1007/s13258-020-00935-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/03/2020] [Indexed: 12/11/2022]
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7
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Casimiro-Soriguer CS, Rubio A, Jimenez J, Pérez-Pulido AJ. Ancient evolutionary signals of protein-coding sequences allow the discovery of new genes in the Drosophila melanogaster genome. BMC Genomics 2020; 21:210. [PMID: 32138644 PMCID: PMC7059364 DOI: 10.1186/s12864-020-6632-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/28/2020] [Indexed: 12/20/2022] Open
Abstract
Background The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive. The number of this kind of genes continuously increases due to new experimental data and development of improved bioinformatics algorithms. Results In this context, AnABlast represents a novel in silico strategy, based on the accumulation of short evolutionary signals identified by protein sequence alignments of low score. This strategy potentially highlights protein-coding regions in genomic sequences regardless of traditional homology or translation signatures. Here, we analyze the evolutionary information that the accumulation of these short signals encloses. Using the Drosophila melanogaster genome, we stablish optimal parameters for the accurate gene prediction with AnABlast and show that this new strategy significantly contributes to add genes, exons and pseudogenes regions, yet to be discovered in both already annotated and new genomes. Conclusions AnABlast can be freely used to analyze genomic regions of whole genomes where it contributes to complete the previous annotation.
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Affiliation(s)
- Carlos S Casimiro-Soriguer
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Alejandro Rubio
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Juan Jimenez
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Antonio J Pérez-Pulido
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain.
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8
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Zhai LL, Zhou J, Zhang J, Tang X, Zhou LY, Yin JY, Vanessa MED, Peng W, Lin J, Deng ZQ. Down-regulation of pseudogene Vimentin 2p is associated with poor outcome in de novo acute myeloid leukemia. Cancer Biomark 2017; 18:305-312. [PMID: 28106537 DOI: 10.3233/cbm-160247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVES This study was intended to investigate the expression status of Vimentin 2p (VIM 2p), a pseudogene of Vimentin, and further analyze its clinical significance in AML patients. METHODS Real-time quantitative PCR (RQ-PCR) was employed to explore the expression status of VIM 2p in 128 patients with de novo AML and 36 healthy controls. RESULTS The expression level of VIM 2p was significantly decreased compared with healthy controls (P< 0.001). The patients with low VIM 2p expression were identified in 93 of 128 (73%) of AML patients. No significant differences could be observed in sex, age, blood parameters, FAB/WHO subtypes, karyotype risks and ten gene mutations (FLT3-ITD, NPM1, C-KIT, IDH1/IDH2, DNMT3 A, C/EBPA, N/K-RAS and U2AF1) between VIM 2p low-expressed and high-expressed patients (P> 0.05). Patients with low VIM 2p expression had significantly shorter overall survival (OS) than those with high VIM 2p expression in whole AML cases (median 7 vs. 13 months, respectively, P= 0.032), besides cytogenetically normal AML (CN-AML) and non-M3 AML cohort (P= 0.042 and 0.045, respectively). CONCLUSIONS These findings indicate that VIM 2p down-regulation is a common event in AML and may be associated with poor clinical outcome.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers
- Biomarkers, Tumor
- Case-Control Studies
- Female
- Gene Expression Regulation, Leukemic
- Humans
- Karyotype
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Male
- Middle Aged
- Mutation
- Nucleophosmin
- Prognosis
- Pseudogenes
- ROC Curve
- Survival Analysis
- Vimentin/genetics
- Young Adult
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9
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An Y, Furber KL, Ji S. Pseudogenes regulate parental gene expression via ceRNA network. J Cell Mol Med 2017; 21:185-192. [PMID: 27561207 PMCID: PMC5192809 DOI: 10.1111/jcmm.12952] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/14/2016] [Indexed: 12/14/2022] Open
Abstract
The concept of competitive endogenous RNA (ceRNA) was first proposed by Salmena and colleagues. Evidence suggests that pseudogene RNAs can act as a 'sponge' through competitive binding of common miRNA, releasing or attenuating repression through sequestering miRNAs away from parental mRNA. In theory, ceRNAs refer to all transcripts such as mRNA, tRNA, rRNA, long non-coding RNA, pseudogene RNA and circular RNA, because all of them may become the targets of miRNA depending on spatiotemporal situation. As binding of miRNA to the target RNA is not 100% complementary, it is possible that one miRNA can bind to multiple target RNAs and vice versa. All RNAs crosstalk through competitively binding to miRNAvia miRNA response elements (MREs) contained within the RNA sequences, thus forming a complex regulatory network. The ratio of a subset of miRNAs to the corresponding number of MREs determines repression strength on a given mRNA translation or stability. An increase in pseudogene RNA level can sequester miRNA and release repression on the parental gene, leading to an increase in parental gene expression. A massive number of transcripts constitute a complicated network that regulates each other through this proposed mechanism, though some regulatory significance may be mild or even undetectable. It is possible that the regulation of gene and pseudogene expression occurring in this manor involves all RNAs bearing common MREs. In this review, we will primarily discuss how pseudogene transcripts regulate expression of parental genes via ceRNA network and biological significance of regulation.
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Affiliation(s)
- Yang An
- Department of Biochemistry and Molecular BiologyMedical SchoolHenan UniversityHenan ProvinceChina
| | - Kendra L. Furber
- College of Pharmacy and NutritionUniversity of SaskatchewanSaskatchewanSKCanada
| | - Shaoping Ji
- Department of Biochemistry and Molecular BiologyMedical SchoolHenan UniversityHenan ProvinceChina
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10
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Prieto-Godino LL, Rytz R, Bargeton B, Abuin L, Arguello JR, Dal Peraro M, Benton R. Olfactory receptor pseudo-pseudogenes. Nature 2016; 539:93-97. [PMID: 27776356 PMCID: PMC5164928 DOI: 10.1038/nature19824] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 09/06/2016] [Indexed: 02/05/2023]
Abstract
Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. Although certain pseudogene-derived RNAs have regulatory roles, and some pseudogene fragments are translated, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, which reflect low selection pressures on loci no longer relevant to the fitness of a species. Here we report the characterization of a pseudogene in the chemosensory variant ionotropic glutamate receptor repertoire of Drosophila sechellia, an insect endemic to the Seychelles that feeds almost exclusively on the ripe fruit of Morinda citrifolia. This locus, D. sechellia Ir75a, bears a premature termination codon (PTC) that appears to be fixed in the population. However, D. sechellia Ir75a encodes a functional receptor, owing to efficient translational read-through of the PTC. Read-through is detected only in neurons and is independent of the type of termination codon, but depends on the sequence downstream of the PTC. Furthermore, although the intact Drosophila melanogaster Ir75a orthologue detects acetic acid-a chemical cue important for locating fermenting food found only at trace levels in Morinda fruit-D. sechellia Ir75a has evolved distinct odour-tuning properties through amino-acid changes in its ligand-binding domain. We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such 'pseudo-pseudogenes' could represent a widespread phenomenon.
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Affiliation(s)
- Lucia L. Prieto-Godino
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Raphael Rytz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Benoîte Bargeton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Liliane Abuin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - J. Roman Arguello
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
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