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Wang X, Wu F, Deng Y, Chai J, Zhang Y, He G, Li X. Increased expression of PSME2 is associated with clear cell renal cell carcinoma invasion by regulating BNIP3‑mediated autophagy. Int J Oncol 2021; 59:106. [PMID: 34779489 PMCID: PMC8651225 DOI: 10.3892/ijo.2021.5286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/11/2021] [Indexed: 02/05/2023] Open
Abstract
Previous studies have showed that proteasome activator complex subunit 2 (PSME2) may play a role in some types of cancer. However, the involvement of PSME2 in clear cell renal cell carcinoma (ccRCC) remains unknown. The aim of the present study was to assess the poorly understood function of PSME2 expression in renal carcinoma. Using bioinformatics analysis, PSME2 mRNA expression profiles were investigated, along with its potential prognostic value and its functional enrichment. Signaling pathways and putative hub genes associated with PSME2 in ccRCC were identified. Based on the bioinformatics analysis results, immunohistochemistry of human ccRCC samples and renal carcinoma cell lines (CAKI-1 and 786-O) transfected with short interfering RNA targeting PSME2 were analyzed using western blot analysis, reverse transcription-quantitative PCR, immunofluorescence, and Cell Counting Kit-8, Transwell and transmission electron microscope assays. The results showed that when PSME2 expression was knocked down, the invasive abilities of the tumor cell lines were reduced, while autophagy was enhanced. The present study demonstrated that PSME2 was associated with the invasion ability of ccRCC cell lines by inhibiting BNIP3-mediated autophagy. In summary, PSME2 could be used as a prognostic factor and a promising therapeutic target in ccRCC.
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Affiliation(s)
- Xiaoyun Wang
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Fengbo Wu
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Yutong Deng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, P.R. China
| | - Jinlong Chai
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Yuehua Zhang
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Gu He
- State Key Laboratory of Biotherapy and Department of Pharmacy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
| | - Xiang Li
- Department of Urology, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, P.R. China
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2
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Yu D, Shi W, Zhang YE. Underrepresentation of active histone modification marks in evolutionarily young genes. INSECT SCIENCE 2017; 24:174-186. [PMID: 26607206 DOI: 10.1111/1744-7917.12299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
It is known that evolutionarily new genes can rapidly evolve essential roles in fundamental biological processes. Nevertheless, the underlying molecular mechanism of how they acquire their novel transcriptional pattern is less characterized except for the role of cis-regulatory evolution. Epigenetic modification offers an alternative possibility. Here, we examined how histone modifications have changed among different gene age groups in Drosophila melanogaster by integrative analyses of an updated new gene dataset and published epigenomic data. We found a robust pattern across various datasets where both the coverage and intensity of active histone modifications, histone 3 lysine 4 trimethylation and lysine 36 trimethylation, increased with evolutionary age. Such a temporal correlation is negative and much weaker for the repressive histone mark, lysine 9 trimethylation, which is expected given its major association with heterochromatin. By further comparison with neighboring old genes, the depletion of active marks of new genes could be only partially explained by the local epigenetic context. All these data are consistent with the observation that older genes bear relatively higher expression levels and suggest that the evolution of histone modifications could be implicated in transcriptional evolution after gene birth.
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Affiliation(s)
- Daqi Yu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenwen Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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3
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Oliver KR, Greene WK. Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis. Ecol Evol 2012; 2:2912-33. [PMID: 23170223 PMCID: PMC3501640 DOI: 10.1002/ece3.400] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 09/11/2012] [Accepted: 09/17/2012] [Indexed: 12/17/2022] Open
Abstract
In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. “Adaptive potential” and “evolutionary potential” are proposed as the extremes of a continuum of “intra-genomic potential” due to TE-Thrust. Specific data is given, indicating “adaptive potential” being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of “evolutionary potential” is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.
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Affiliation(s)
- Keith R Oliver
- School of Biological Science and Biotechnology, Faculty of Science and Engineering, Murdoch University Perth, W.A., 6150, Australia
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4
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Abstract
Ever since the pre-molecular era, the birth of new genes with novel functions has been considered to be a major contributor to adaptive evolutionary innovation. Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. Indeed, recent work has provided initial whole-genome views of the different types of new genes for a large number of different organisms. The array of mechanisms underlying the origin of new genes is compelling, extending way beyond the traditionally well-studied source of gene duplication. Thus, it was shown that novel genes also regularly arose from messenger RNAs of ancestral genes, protein-coding genes metamorphosed into new RNA genes, genomic parasites were co-opted as new genes, and that both protein and RNA genes were composed from scratch (i.e., from previously nonfunctional sequences). These mechanisms then also contributed to the formation of numerous novel chimeric gene structures. Detailed functional investigations uncovered different evolutionary pathways that led to the emergence of novel functions from these newly minted sequences and, with respect to animals, attributed a potentially important role to one specific tissue--the testis--in the process of gene birth. Remarkably, these studies also demonstrated that novel genes of the various types significantly impacted the evolution of cellular, physiological, morphological, behavioral, and reproductive phenotypic traits. Consequently, it is now firmly established that new genes have indeed been major contributors to the origin of adaptive evolutionary novelties.
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Affiliation(s)
- Henrik Kaessmann
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.
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Unique functions of repetitive transcriptomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 285:115-88. [PMID: 21035099 DOI: 10.1016/b978-0-12-381047-2.00003-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Repetitive sequences occupy a huge fraction of essentially every eukaryotic genome. Repetitive sequences cover more than 50% of mammalian genomic DNAs, whereas gene exons and protein-coding sequences occupy only ~3% and 1%, respectively. Numerous genomic repeats include genes themselves. They generally encode "selfish" proteins necessary for the proliferation of transposable elements (TEs) in the host genome. The major part of evolutionary "older" TEs accumulated mutations over time and fails to encode functional proteins. However, repeats have important functions also on the RNA level. Repetitive transcripts may serve as multifunctional RNAs by participating in the antisense regulation of gene activity and by competing with the host-encoded transcripts for cellular factors. In addition, genomic repeats include regulatory sequences like promoters, enhancers, splice sites, polyadenylation signals, and insulators, which actively reshape cellular transcriptomes. TE expression is tightly controlled by the host cells, and some mechanisms of this regulation were recently decoded. Finally, capacity of TEs to proliferate in the host genome led to the development of multiple biotechnological applications.
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Gogvadze E, Buzdin A. Retroelements and their impact on genome evolution and functioning. Cell Mol Life Sci 2009; 66:3727-42. [PMID: 19649766 PMCID: PMC11115525 DOI: 10.1007/s00018-009-0107-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/11/2009] [Accepted: 07/14/2009] [Indexed: 12/31/2022]
Abstract
Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.
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Affiliation(s)
- Elena Gogvadze
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya st, 117997 Moscow, Russia.
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Affiliation(s)
- Henrik Kaessmann
- Center for Integrative Genomics, University of Lausanne, Genopode Building, CH-1015 Lausanne, Switzerland.
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8
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Abstract
Gene copies that stem from the mRNAs of parental source genes have long been viewed as evolutionary dead-ends with little biological relevance. Here we review a range of recent studies that have unveiled a significant number of functional retroposed gene copies in both mammalian and some non-mammalian genomes. These studies have not only revealed previously unknown mechanisms for the emergence of new genes and their functions but have also provided fascinating general insights into molecular and evolutionary processes that have shaped genomes. For example, analyses of chromosomal gene movement patterns via RNA-based gene duplication have shed fresh light on the evolutionary origin and biology of our sex chromosomes.
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Bai Y, Casola C, Betrán E. Evolutionary origin of regulatory regions of retrogenes in Drosophila. BMC Genomics 2008; 9:241. [PMID: 18498650 PMCID: PMC2413143 DOI: 10.1186/1471-2164-9-241] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 05/22/2008] [Indexed: 12/29/2022] Open
Abstract
Background Retrogenes are processed copies of other genes. This duplication mechanism produces a copy of the parental gene that should not contain introns, and usually does not contain cis-regulatory regions. Here, we computationally address the evolutionary origin of promoter and other cis-regulatory regions in retrogenes using a total of 94 Drosophila retroposition events we recently identified. Previous tissue expression data has revealed that a large fraction of these retrogenes are specifically and/or highly expressed in adult testes of Drosophila. Results In this work, we infer that retrogenes do not generally carry regulatory regions from aberrant upstream or normal transcripts of their parental genes, and that expression patterns of neighboring genes are not consistently shared by retrogenes. Additionally, transposable elements do not appear to substantially provide regulatory regions to retrogenes. Interestingly, we find that there is an excess of retrogenes in male testis neighborhoods that is not explained by insertional biases of the retroelement machinery used for retroposition. Conclusion We conclude that retrogenes' regulatory regions mostly do not represent a random set of existing regulatory regions. On the contrary, our conclusion is that selection is likely to have played an important role in the persistence of autosomal testis biased retrogenes. Selection in favor of retrogenes inserted in male testis neighborhoods and at the sequence level to produce testis expression is postulated to have occurred.
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Affiliation(s)
- Yongsheng Bai
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
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Girardot M, Guibert S, Laforet MP, Gallard Y, Larroque H, Oulmouden A. The insertion of a full-length Bos taurus LINE element is responsible for a transcriptional deregulation of the Normande Agouti gene. ACTA ACUST UNITED AC 2006; 19:346-55. [PMID: 16827753 DOI: 10.1111/j.1600-0749.2006.00312.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mammalian pigmentation is controlled by the concerted action of Tyr, Tyrp1 and Dct producing eumelanin and/or pheomelanin in melanocytes. The ratio of these two pigments is determined by the agonist alpha-melanocyte stimulating hormone and the antagonist Agouti protein acting on the Mc1r. Here we show that the Agouti gene is over-expressed in Normande breed compared with Prim'Holstein breed. The Normande cattle have a characteristic coat color phenotype with a variable presence of black (eumelanin) hair over a red/brown background. We have found a previously undescribed full-length L1-BT element inserted in the 5'-genomic sequence of the Agouti gene in Normande cattle which promotes the over-expression of alternative transcripts. The variable expression of the alternative transcript directed by the long interspersed nuclear element promoter may be the origin of the brindle coat color pattern of the Normande breed. This new bovine Agouti allele isolated in Normande breed has been named Abr. Finally, as ectopic over-expression of Agouti in Ay mice is responsible for the obesity syndrome, we discuss the possible consequences of Abr for meat and milk production in cattle.
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Affiliation(s)
- Michael Girardot
- Unité de Génétique Moléculaire Animale, UMR 1061-INRA/Université de Limoges, Limoges, France
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11
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von Sternberg R, Shapiro JA. How repeated retroelements format genome function. Cytogenet Genome Res 2005; 110:108-16. [PMID: 16093662 DOI: 10.1159/000084942] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2004] [Accepted: 08/03/2004] [Indexed: 11/19/2022] Open
Abstract
Genomes operate as sophisticated information storage systems. Generic repeated signals in the DNA format expression of coding sequence files and organize additional functions essential for genome replication and accurate transmission to progeny cells. Retroelements comprise a major fraction of many genomes and contain a surprising diversity of functional signals. In this article, we summarize some features of the taxonomic distribution of retroelements, especially mammalian SINEs, tabulate functional roles documented for different classes of retroelements, and discuss their potential roles as genome organizers. In particular, the fact that certain retroelements serve as boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the reversed transcribed component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the "functionalist" perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization.
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Affiliation(s)
- R von Sternberg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
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12
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Abstract
There are clear theoretical reasons and many well-documented examples which show that repetitive, DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the 'functionalist' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA.
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Murata S, Udono H, Tanahashi N, Hamada N, Watanabe K, Adachi K, Yamano T, Yui K, Kobayashi N, Kasahara M, Tanaka K, Chiba T. Immunoproteasome assembly and antigen presentation in mice lacking both PA28alpha and PA28beta. EMBO J 2001; 20:5898-907. [PMID: 11689430 PMCID: PMC125708 DOI: 10.1093/emboj/20.21.5898] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Two members of the proteasome activator, PA28alpha and PA28beta, form a heteropolymer that binds to both ends of the 20S proteasome. Evidence in vitro indicates that this interferon-gamma (IFN-gamma)-inducible heteropolymer is involved in the processing of intracellular antigens, but its functions in vivo remain elusive. To investigate the role of PA28alpha/beta in vivo, we generated mice deficient in both PA28alpha and PA28beta genes. The ATP-dependent proteolytic activities were decreased in PA28alpha(-/-)/beta(-/-) cells, suggesting that 'hybrid proteasomes' are involved in protein degradation. Treatment of PA28alpha(-/-)/beta(-/-) cells with IFN-gamma resulted in sufficient induction of the 'immunoproteasome'. Moreover, splenocytes from PA28alpha(-/-)/beta(-/-) mice displayed no apparent defects in processing of ovalbumin. These results are in marked contrast to the previous finding that immunoproteasome assembly and immune responses were impaired in PA28beta(-/-) mice. PA28alpha(-/-)/beta(-/-) mice also showed apparently normal immune responses against infection with influenza A virus. However, they almost completely lost the ability to process a melanoma antigen TRP2-derived peptide. Hence, PA28alpha/beta is not a prerequisite for antigen presentation in general, but plays an essential role for the processing of certain antigens.
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Affiliation(s)
| | - Heiichiro Udono
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
| | | | - Nobuyuki Hamada
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
| | - Ken Watanabe
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
| | - Kei Adachi
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
| | - Taketoshi Yamano
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
| | - Katsuyuki Yui
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
| | - Nobuyuki Kobayashi
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
| | - Masanori Kasahara
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
| | | | - Tomoki Chiba
- Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, and CREST, Japan Science and Technology Corporation, Tokyo 113-8613,
Department of Medical Zoology and Immunology, School of Medicine and Laboratory of Molecular Biology of Diseases, School of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8521 and Department of Biosystems Science, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama 240-0193, Japan Corresponding author e-mail:
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Abstract
There are two immune responses in vertebrates: humoral immunity is mediated by circulating antibodies, whereas cytotoxic T lymphocytes (CTL) confer cellular immunity. CTL lyse infected cells upon recognition of cell-surface MHC Class I molecules complexed with foreign peptides. The displayed peptides are produced in the cytosol by degradation of host proteins or proteins from intracellular pathogens that might be present. Proteasomes are cylindrical multisubunit proteases that generate many of the peptides eventually transferred to the cell surface for immune surveillance. In mammalian proteasomes, six active sites face a central chamber. As this chamber is sealed off from the enzyme's surface, there must be mechanisms to promote entry of substrates. Two protein complexes have been found to bind the ends of the proteasome and activate it. One of the activators is the 19 S regulatory complex of the 26 S proteasome; the other activator is '11 S REG' [Dubiel, Pratt, Ferrell and Rechsteiner (1992) J. Biol. Chem. 267, 22369-22377] or 'PA28' [Ma, Slaughter and DeMartino (1992) J. Biol. Chem. 267, 10515-10523]. During the past 7 years, our understanding of the structure of REG molecules has increased significantly, but much less is known about their biological functions. There are three REG subunits, namely alpha, beta and gamma. Recombinant REGalpha forms a ring-shaped heptamer of known crystal structure. 11 S REG is a heteroheptamer of alpha and beta subunits. REGgamma is also presumably a heptameric ring, and it is found in the nuclei of the nematode work Caenorhabditis elegans and higher organisms, where it may couple proteasomes to other nuclear components. REGalpha and REGbeta, which are abundant in vertebrate immune tissues, are located mostly in the cytoplasm. Synthesis of REG alpha and beta subunits is induced by interferon-gamma, and this has led to the prevalent hypothesis that REG alpha/beta hetero-oligomers play an important role in Class I antigen presentation. In the present review we focus on the structural properties of REG molecules and on the evidence that REGalpha/beta functions in the Class I immune response.
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Brosius J. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 1999; 238:115-34. [PMID: 10570990 DOI: 10.1016/s0378-1119(99)00227-9] [Citation(s) in RCA: 275] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While the significance of middle repetitive elements had been neglected for a long time, there are again tendencies to ascribe most members of a given middle repetitive sequence family a functional role--as if the discussion of SINE (short interspersed repetitive elements) function only can occupy extreme positions. In this article, I argue that differences between the various classes of retrosequences concern mainly their copy numbers. Consequently, the function of SINEs should be viewed as pragmatic such as, for example, mRNA-derived retrosequences, without underestimating the impact of retroposition for generation of novel protein coding genes or parts thereof (exon shuffling by retroposition) and in particular of SINEs (and retroelements) in modulating genes and their expression. Rapid genomic change by accumulating retrosequences may even facilitate speciation [McDonald, J.F., 1995. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10, 123-126.] In addition to providing mobile regulatory elements, small RNA-derived retrosequences including SINEs can, in analogy to mRNA-derived retrosequences, also give rise to novel small RNA genes. Perhaps not representative for all SINE/master gene relationships, we gained significant knowledge by studying the small neuronal non-messenger RNAs, namely BC1 RNA in rodents and BC200 RNA in primates. BC1 is the first identified master gene generating a subclass of ID repetitive elements, and BC200 is the only known Alu element (monomeric) that was exapted as a novel small RNA encoding gene.
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Affiliation(s)
- J Brosius
- Institute of Experimental Pathology/Molecular Neurobiology, ZMBE, University of Münster, Germany.
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