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Ma H, Wang M, Zhang YE, Tan S. The power of "controllers": Transposon-mediated duplicated genes evolve towards neofunctionalization. J Genet Genomics 2023; 50:462-472. [PMID: 37068629 DOI: 10.1016/j.jgg.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Since the discovery of the first transposon by Dr. Barbara McClintock, the prevalence and diversity of transposable elements (TEs) have been gradually recognized. As fundamental genetic components, TEs drive organismal evolution not only by contributing functional sequences (e.g., regulatory elements or "controllers" as phrased by Dr. McClintock) but also by shuffling genomic sequences. In the latter respect, TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive interest. In response to the development of this field, we herein attempt to provide an overview of TE-mediated duplication by focusing on common rules emerging across duplications generated by different TE types. Specifically, despite the huge divergence of transposition machinery across TEs, we identify three common features of various TE-mediated duplication mechanisms, including end bypass, template switching, and recurrent transposition. These three features lead to one common functional outcome, namely, TE-mediated duplicates tend to be subjected to exon shuffling and neofunctionalization. Therefore, the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these duplicates. We finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.
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Affiliation(s)
- Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengxia Wang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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2
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Attwood MM, Schiöth HB. Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. Front Cell Dev Biol 2020; 7:386. [PMID: 32039202 PMCID: PMC6987440 DOI: 10.3389/fcell.2019.00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/19/2019] [Indexed: 11/13/2022] Open
Abstract
As the structure and functions of proteins are correlated, investigating groups of proteins with the same gross structure may provide important insights about their functional roles. Trispanins, proteins that contain three alpha-helical transmembrane (3TM) regions, have not been previously studied considering their transmembrane features. Our comprehensive identification and classification using bioinformatic methods describe 152 3TM proteins. These proteins are frequently involved in membrane biosynthesis and lipid biogenesis, protein trafficking, catabolic processes, and in particular signal transduction due to the large ionotropic glutamate receptor family. Proteins that localize to intracellular compartments are overrepresented in the dataset in comparison to the entire human transmembrane proteome, and nearly 45% localize specifically to the endoplasmic reticulum (ER). Furthermore, nearly 20% of the trispanins function in lipid metabolic processes and transport, which are also overrepresented. Nearly one-third of trispanins are identified as being targeted by drugs and/or being associated with diseases. A high number of 3TMs have unknown functions and based on this analysis we speculate on the functional involvement of uncharacterized trispanins in relationship to disease or important cellular activities. This first overall study of trispanins provides a unique analysis of a diverse group of membrane proteins.
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Affiliation(s)
- Misty M. Attwood
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B. Schiöth
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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3
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Ishihara S, Dang‐Nguyen TQ, Kikuchi K, Arakawa A, Mikawa S, Osaki M, Otoi T, Luu QM, Nguyen TS, Taniguchi M. Characteristic features of porcine endogenous retroviruses in Vietnamese native pigs. Anim Sci J 2020; 91:e13336. [PMID: 32219916 DOI: 10.1111/asj.13336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/25/2019] [Accepted: 12/06/2019] [Indexed: 12/14/2022]
Abstract
We aimed to clarify the genomic characteristics of porcine endogenous retroviruses (PERVs) in Vietnamese native pig (VnP) breeds. First, we investigated genetic polymorphisms in β- and γ-like PERVs, and we then measured the copy numbers of infectious γ-like PERVs (PERV-A, B, and C). We purified genomic DNA from 15 VnP breeds from 12 regions all over the country and three Western pig breeds as controls, and investigated genetic polymorphisms in all known PERVs, including the beta (β)1-4 and gamma (γ)1-5 groups. PERVs of β1, β2, β3, and γ4 were highly polymorphic with VnP-specific haplotypes. We did not identify genetic polymorphisms in β4, γ1, or γ2 PERVs. We then applied a real-time polymerase chain reaction-based method to estimate copy numbers of the gag, pol, and env genes of γ1 PERVs (defined as A, B, and C). VnP breeds showed significantly lower copy number of the PERV genes compared with the Western pig breeds (on average, 16.2 and 35.7 copies, respectively, p < .05). Two VnP breeds showed significantly higher copy number compared with the other VnPs (p < .05). Our results elucidated that VnPs have specific haplotypes and a low copy number of PERV genes.
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Affiliation(s)
- Shinya Ishihara
- Institute of Agrobiological Sciences National Agriculture and Food Research Organization Tsukuba Japan
| | - Thanh Q. Dang‐Nguyen
- Institute of Agrobiological Sciences National Agriculture and Food Research Organization Tsukuba Japan
| | - Kazuhiro Kikuchi
- Institute of Agrobiological Sciences National Agriculture and Food Research Organization Tsukuba Japan
| | - Aisaku Arakawa
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Japan
| | - Satoshi Mikawa
- Institute of Agrobiological Sciences National Agriculture and Food Research Organization Tsukuba Japan
| | - Makoto Osaki
- National Institute of Animal Health National Agriculture and Food Research Organization Tsukuba Japan
| | - Takeshige Otoi
- Faculty of Bioscience and Bioindustry Tokushima University Tokushima Japan
| | - Quang Minh Luu
- Key Laboratory of Animal Cell Technology National Institute of Animal Science Hanoi Vietnam
| | - Thanh Son Nguyen
- Key Laboratory of Animal Cell Technology National Institute of Animal Science Hanoi Vietnam
| | - Masaaki Taniguchi
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Japan
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4
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Minarovits J, Niller HH. Truncated oncoproteins of retroviruses and hepatitis B virus: A lesson in contrasts. INFECTION GENETICS AND EVOLUTION 2019; 73:342-357. [DOI: 10.1016/j.meegid.2019.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/14/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
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5
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Tan S, Cardoso-Moreira M, Shi W, Zhang D, Huang J, Mao Y, Jia H, Zhang Y, Chen C, Shao Y, Leng L, Liu Z, Huang X, Long M, Zhang YE. LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans. Genome Res 2016; 26:1663-1675. [PMID: 27934698 PMCID: PMC5131818 DOI: 10.1101/gr.204925.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 10/18/2016] [Indexed: 01/09/2023]
Abstract
In a broad range of taxa, genes can duplicate through an RNA intermediate in a process mediated by retrotransposons (retroposition). In mammals, L1 retrotransposons drive retroposition, but the elements responsible for retroposition in other animals have yet to be identified. Here, we examined young retrocopies from various animals that still retain the sequence features indicative of the underlying retroposition mechanism. In Drosophila melanogaster, we identified and de novo assembled 15 polymorphic retrocopies and found that all retroposed loci are chimeras of internal retrocopies flanked by discontinuous LTR retrotransposons. At the fusion points between the mRNAs and the LTR retrotransposons, we identified shared short similar sequences that suggest the involvement of microsimilarity-dependent template switches. By expanding our approach to mosquito, zebrafish, chicken, and mammals, we identified in all these species recently originated retrocopies with a similar chimeric structure and shared microsimilarities at the fusion points. We also identified several retrocopies that combine the sequences of two or more parental genes, demonstrating LTR-retroposition as a novel mechanism of exon shuffling. Finally, we found that LTR-mediated retrocopies are immediately cotranscribed with their flanking LTR retrotransposons. Transcriptional profiling coupled with sequence analyses revealed that the sense-strand transcription of the retrocopies often lead to the origination of in-frame proteins relative to the parental genes. Overall, our data show that LTR-mediated retroposition is highly conserved across a wide range of animal taxa; combined with previous work from plants and yeast, it represents an ancient and ongoing mechanism continuously shaping gene content evolution in eukaryotes.
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Affiliation(s)
- Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Wenwen Shi
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Huang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Mao
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hangxing Jia
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaqiong Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Shao
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Leng
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhonghua Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Abstract
Holistic emerging approaches allow us to understand that every organism is the result of integration mechanisms observed at every level of nature: integration of DNA from virus and bacteria in metazoans, endosymbiotic relationships and holobionts. Horizontal gene transfer events in Bacteria, Archaea and Eukaryotes have resulted in the chimeric nature of genomes. As a continuity of this genomic landscape, the human body contains more bacterial than human cells. Human microbiome has co-evolved with the human being as a unity called holobiont. The loss of part of our microbiome along evolution can explain the continuous increasing incidence of immune and inflammatory-related diseases. Life is a continuous process in which the organism experiences its environment and this interaction impacts in the epigenetic system and the genomic structure. The emerging perspectives restitute the great importance of Lamarck's theoretical contributions (the milieu) and Darwin's pangenesis theory.
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7
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Garcia-Etxebarria K, Jugo BM. Genomic environment and digital expression of bovine endogenous retroviruses. Gene 2014; 548:14-21. [DOI: 10.1016/j.gene.2014.06.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 02/08/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
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8
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Salvucci E. Selfishness, warfare, and economics; or integration, cooperation, and biology. Front Cell Infect Microbiol 2012; 2:54. [PMID: 22919645 PMCID: PMC3417387 DOI: 10.3389/fcimb.2012.00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 04/06/2012] [Indexed: 12/11/2022] Open
Abstract
The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. It is necessary to discuss the explaining power of the dominant paradigm. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. In addition to the discussion on the validity of natural selection, modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related to the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: viruses are recognized as a macroorganism with a huge collection of genes, most unknown that constitute the major planet's gene pool. They play a fundamental role in evolution since their sequences are capable of integrating into the genomes in an “infective” way and become an essential part of multicellular organisms. They have content with “biological sense” i.e., they appear as part of normal life processes and have a serious role as carrier elements of complex genetic information. Antibiotics are cell signals with main effects on general metabolism and transcription on bacterial cells and communities. The hologenome theory considers an organism and all of its associated symbiotic microbes (parasites, mutualists, synergists, amensalists) as a result of symbiopoiesis. Microbes, helmints, that are normally understood as parasites are cohabitants and they have cohabited with their host and drive the evolution and existence of the partners. Each organism is the result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial, virus, and eukaryotic DNA and it is the result of the interaction of its own genome with the genome of its microbiota, and their metabolism are intertwined (as a “superorganism”) along evolution. The darwinian paradigm had its origin in the free market theories and concepts of Malthus and Spencer. Then, nature was explained on the basis of market theories moving away from an accurate explanation of natural phenomena. It is necessary to acknowledge the limitations of the dominant dogma. These new interpretations about biological processes, molecules, roles of viruses in nature, and microbial interactions are remarkable points to be considered in order to construct a solid theory adjusted to the facts and with less speculations and tortuous semantic traps.
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Affiliation(s)
- Emiliano Salvucci
- Consejo Nacional de Investigaciones Cientificas y Técnicas Argentina.
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9
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Ha HS, Chung WK, Ahn K, Bae JH, Park SJ, Moon JW, Nam KH, Han K, Cho HG, Kim HS. Development of GEBRET: a web-based analysis tool for retroelements in primate genomes. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0103-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Abstract
The capacity to integrate into the chromosomal DNA of germ-line cells has endowed retroviruses with the potential to be vertically transmitted from generation to generation and eventually become fixed in the genomes of the entire population. This has been independently accomplished by several ancient retroviruses that invaded the genomes of our early and more recent primate and hominoid ancestors. Some of the inherited elements then proliferated in the genome, resulting in a number of lineages with complex phylogenetic patterns. Although the vast majority of chromosomally integrated retroelements have suffered inactivating mutations and deletions, a significant impact on various aspects of human biology has been recently revealed and evidence for the present activity of at least one human endogenous retrovirus family continues to accumulate.
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11
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Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 2008; 60:1-18. [PMID: 18193213 PMCID: PMC2206249 DOI: 10.1007/s00251-007-0262-2] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/29/2007] [Indexed: 02/05/2023]
Abstract
The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.
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Lerat E, Birot AM, Samarut J, Mey A. Maintenance in the Chicken Genome of the Retroviral-like cENS Gene Family Specifically Expressed in Early Embryos. J Mol Evol 2007; 65:215-27. [PMID: 17671751 DOI: 10.1007/s00239-007-9001-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 05/18/2007] [Indexed: 02/05/2023]
Abstract
Embryonic stem (ES) cells are important developmental cells that appear very early during development and subsequently give rise to all the cell lineages of the future adult organism. In these cells a limited subset of transcription factors is expressed that are well conserved among species and essential for the fate of the stem cell. The transcriptome analysis of ES cells from chicken has revealed a gene family, cENS, that is specifically expressed in ES cells and in early embryos and is repressed during the differentiation process. This family is characterized by displaying retroviral structures and shares no homology with other species' genes. These characteristics are probably not restricted to the chicken genome and raise the question of whether similar genes are present and have been maintained in other species. We have examined the different copies of this gene in the sequenced chicken genome to investigate its dynamics and its evolution. We have distinguished two groups of cENS-related copies. The first group, resulting from recent transposition events, contains the transcribed ENS-1 and ENS-3 plus copies subjected to negative selection pressures. The second group contains degenerate copies that were integrated into the genome earlier. Comparison with copies previously isolated from three Galliformes showed that they are also subjected to selection pressures. We also detected numerous solo-LTRs containing the ENS-1 promoter that may control the expression of host genes. Taken together, these findings suggest a function sustained by a neogene of retroviral origin during the early stages of chicken development.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France.
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13
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Buzdin A, Gogvadze E, Lebrun MH. Chimeric retrogenes suggest a role for the nucleolus in LINE amplification. FEBS Lett 2007; 581:2877-82. [DOI: 10.1016/j.febslet.2007.05.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 05/03/2007] [Accepted: 05/16/2007] [Indexed: 01/21/2023]
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14
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Huh JW, Kim TH, Yi JM, Park ES, Kim WY, Sin HS, Kim DS, Min DS, Kim SS, Kim CB, Hyun BH, Kang SK, Jung JS, Lee WH, Takenaka O, Kim HS. Molecular Evolution of the Periphilin Gene in Relation to Human Endogenous Retrovirus M Element. J Mol Evol 2006; 62:730-7. [PMID: 16612547 DOI: 10.1007/s00239-005-0109-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Accepted: 01/12/2006] [Indexed: 10/24/2022]
Abstract
HERV-M (human endogenous retrovirus M), related to the super family of HERV-K, has a methionine (M) tRNA primer-binding site, and is located within the periphilin gene on human chromosome 12q12. HERV-M has been integrated into the periphilin gene as the truncated form, 5'LTR-gag-pol-3'LTR. Polymerase chain reaction (PCR) and reverse transcription-polymerase chain reaction (RT-PCR) approaches were conducted to investigate its evolutionary origins. Interestingly, the insertion of retroelements in a common ancestor genome can make different transcript variants in different species. In the case of the periphilin gene, human (10 variants) and mouse (2 variants) lineages show different transcript variants. Insertion of HERV-M (variant 1-3) could affect the protein-coding region. Also, Alusq/x (variant 4-9) and L1ME4a (mammalian-wide subfamilies of LINE-1) (variant 10) in humans and SINE (short interspersed repetitive element) and RLTR15 (the mouse putative long terminal repeat) (variant 2) in mice could be driving forces in transcript diversification of the periphilin gene during mammalian evolution. The HERV-M derived transcripts (variant 1-3) were expressed in different human tissues, whereas they were not detected in crab-eating monkey and squirrel monkey tissues by RT-PCR amplification. Taken together, HERV-M seems to have been integrated into our common ancestor genome after the divergence of simians and prosimians, and then was actively expressed during hominoid evolution.
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Affiliation(s)
- Jae-Won Huh
- Division of Biological Sciences, College of Natural Sciences, Pusan National University, Pusan, Korea
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15
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Pavlicek A, Gentles AJ, Pačes J, Pačes V, Jurka J. Retroposition of processed pseudogenes: the impact of RNA stability and translational control. Trends Genet 2005; 22:69-73. [PMID: 16356584 PMCID: PMC1379630 DOI: 10.1016/j.tig.2005.11.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 09/30/2005] [Accepted: 11/16/2005] [Indexed: 11/17/2022]
Abstract
Human processed pseudogenes are copies of cellular RNAs reverse transcribed and inserted into the nuclear genome by the enzymatic machinery of L1 (LINE1) non-LTR retrotransposons. Although it is generally accepted that germline expression is crucial for the heritable retroposition of cellular mRNAs, little is known about the influences of RNA stability, mRNA quality control and compartmentalization of translation on the retroposition of processed pseudogenes. We found that frequently retroposed human mRNAs are derived from stable transcripts with translation-competent functional reading frames that are resistant to nonsense-mediated RNA decay. They are preferentially translated on free cytoplasmic ribosomes and encode soluble proteins. Our results indicate that interactions between mRNAs and L1 proteins seem to occur at free cytoplasmic ribosomes.
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Affiliation(s)
- Adam Pavlicek
- Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
| | - Andrew J. Gentles
- Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
| | - Jan Pačes
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo 2, Prague CZ-16637, Czech Republic
| | - Václav Pačes
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo 2, Prague CZ-16637, Czech Republic
| | - Jerzy Jurka
- Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
- * To whom correspondence should be addressed. E-mail: (JJ)
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16
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Brosius J. Echoes from the past--are we still in an RNP world? Cytogenet Genome Res 2005; 110:8-24. [PMID: 16093654 DOI: 10.1159/000084934] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Accepted: 05/04/2004] [Indexed: 11/19/2022] Open
Abstract
Availability of the human genome sequence and those of other species is unmeasured in their value for a comprehensive understanding of the architecture, function and evolution of genomes and cells. Various mechanisms keep genomes in flux and generate intra- and interspecies variation. The conversion of RNA modules into DNA and their more or less random integration into chromosomes (retroposition) is in many lineages including our own the most pervasive and perhaps the most enigmatic. The proclivity of such events in extant multicellular eukaryotes, even in more recent evolutionary times, gives the impression that the transition period from the RNP (ribonucleoprotein) world to the emergence of modern cells, where DNA became the predominant carrier of genetic information, has lasted billions of years and is an endlessly drawn-out process rather than the punctuated event one might expect. Apart from the impact of such RNA-mediated processes as retroposition, the role of RNA in a wide variety of cellular functions has only recently become more widely appreciated.
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Affiliation(s)
- J Brosius
- Institute of Experimental Pathology, ZMBE, University of Munster, Munster, Germany.
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17
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Medstrand P, van de Lagemaat LN, Dunn CA, Landry JR, Svenback D, Mager DL. Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res 2005; 110:342-52. [PMID: 16093686 DOI: 10.1159/000084966] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Accepted: 01/07/2004] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are present in all organisms and nearly half of the human and mouse genome is derived from ancient transpositions. This fact alone suggests that TEs have played a major role in genome organization and evolution. Studies undertaken over the last two decades or so clearly show that TEs of various kinds have played an important role in organism evolution. Here we review the impact TEs have on the evolution of gene regulation and gene function with an emphasis on humans. Understanding the mechanisms resulting in genomic change is central to our understanding of gene regulation, genetic disease and genome evolution. Full comprehension of these biological processes is not possible without an in depth knowledge of how TEs impact upon the genome.
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Affiliation(s)
- P Medstrand
- Department of Cell and Molecular Biology, Biomedical Centre, Lund University, Lund, Sweden.
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Gogvadze EV, Buzdin AA, Sverdlov ED. [Multiple template switches on LINE-directed reverse transcription: the most probable formation mechanism for the double and triple chimeric retroelements in mammals]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2005; 31:82-9. [PMID: 15787218 DOI: 10.1007/s11171-005-0010-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
It was shown that the shuffling mechanism for transcribed genome components, which involves a template switch on the RNA reverse transcription using the L1 retroelement enzymatic machinery, is common in mammals. The occurrence frequency of the resulting chimeric retroelements in the genomes of rodents is twice as high as in the DNA of primates. Moreover, we proved that not only single but also double switches may occur in vivo, which result in the fusion of copies of three different transcripts. Many of the identified chimeras are transcribed in mammals.
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Delgado S, Girondot M, Sire JY. Molecular evolution of amelogenin in mammals. J Mol Evol 2005; 60:12-30. [PMID: 15696365 DOI: 10.1007/s00239-003-0070-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Accepted: 07/21/2004] [Indexed: 10/25/2022]
Abstract
An evolutionary analysis of mammalian amelogenin, the major protein of forming enamel, was conducted by comparison of 26 sequences (including 14 new ones) representative of the main mammalian lineages. Amelogenin shows highly conserved residues in the hydrophilic N- and C-terminal regions. The central hydrophobic region (most of exon 6) is more variable, but it has conserved a high amount of proline and glutamine located in triplets, PXQ, indicating that these residues play an important role. This region evolves more rapidly, and is less constrained, than the other well-conserved regions, which are subjected to strong constraints. The comparison of the substitution rates in relation to the CpG richness confirmed that the highly conserved regions are subjected to strong selective pressures. The amino acids located at important sites and the residues known to lead to amelogenesis imperfecta when substituted were present in all sequences examined. Evolutionary analysis of the variable region of exon 6 points to a particular zone, rich in either amino acid insertion or deletion. We consider this region a hot spot of mutation for the mammalian amelogenin. In this region, numerous triplet repeats (PXQ) have been inserted recently and independently in five lineages, while most of the hydrophobic exon 6 region probably had its origin in several rounds of triplet insertions, early in vertebrate evolution. The putative ancestral DNA sequence of the mammalian amelogenin was calculated using a maximum likelihood approach. The putative ancestral protein was composed of 177 residues. It already contained all important amino acid positions known to date, its hydrophobic variable region was rich in proline and glutamine, and it contained triplet repeats PXQ as in the modern sequences.
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Affiliation(s)
- Sidney Delgado
- FRE2696, Equipe Evolution & Développement du Squelette, Université Paris 6, Paris, France
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A New Mechanism of Retrogene Formation in Mammalian Genomes: In Vivo Recombination during RNA Reverse Transcription. Mol Biol 2005. [DOI: 10.1007/s11008-005-0045-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Flockerzi A, Burkhardt S, Schempp W, Meese E, Mayer J. Human endogenous retrovirus HERV-K14 families: status, variants, evolution, and mobilization of other cellular sequences. J Virol 2005; 79:2941-9. [PMID: 15709013 PMCID: PMC548434 DOI: 10.1128/jvi.79.5.2941-2949.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human genome harbors many distinct families of human endogenous retroviruses (HERVs) that stem from exogenous retroviruses that infected the germ line millions of years ago. Many HERV families remain to be investigated. We report in the present study the detailed characterization of the HERV-K14I and HERV-K14CI families as they are represented in the human genome. Most of the 68 HERV-K14I and 23 HERV-K14CI proviruses are severely mutated, frequently displaying uniform deletions of retroviral genes and long terminal repeats (LTRs). Both HERV families entered the germ line approximately 39 million years ago, as evidenced by homologous sequences in hominoids and Old World primates and calculation of evolutionary ages based on a molecular clock. Proviruses of both families were formed during a brief period. A majority of HERV-K14CI proviruses on the Y chromosome mimic a higher evolutionary age, showing that LTR-LTR divergence data can indicate false ages. Fully translatable consensus sequences encoding major retroviral proteins were generated. Most HERV-K14I loci lack an env gene and are structurally reminiscent of LTR retrotransposons. A minority of HERV-K14I variants display an env gene. HERV-K14I proviruses are associated with three distinct LTR families, while HERV-K14CI is associated with a single LTR family. Hybrid proviruses consisting of HERV-K14I and HERV-W sequences that appear to have produced provirus progeny in the genome were detected. Several HERV-K14I proviruses harbor TRPC6 mRNA portions, exemplifying mobilization of cellular transcripts by HERVs. Our analysis contributes essential information on two more HERV families and on the biology of HERV sequences in general.
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Affiliation(s)
- Aline Flockerzi
- Department of Human Genetics, Building 60, University of Saarland, 66421 Homburg, Germany
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Niller HH, Salamon D, Rahmann S, Ilg K, Koroknai A, Bánáti F, Schwarzmann F, Wolf H, Minárovits J. A 30 kb region of the Epstein-Barr virus genome is colinear with the rearranged human immunoglobulin gene loci: implications for a "ping-pong evolution" model for persisting viruses and their hosts. A review. Acta Microbiol Immunol Hung 2004; 51:469-84. [PMID: 15704335 DOI: 10.1556/amicr.51.2004.4.7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The left part of the Epstein-Barr virus (EBV) genome exhibits a strong colinearity of structural and functional elements with the immunoglobulin (Ig) gene loci which is only partially reflected in nucleotide sequence homologies. We propose that this colinearity may be the result of an inter-dependent co-evolution of the immunoglobulin loci together with EBV. Our observation could help elucidating the mechanisms of somatic hypermutation, explaining the ability of EBV to accidentally cause tumors, and shedding more light on the general mechanisms of viral and organismal evolution. We suggest that persisting viruses served as a complement for the organismal germline like in a ping-pong game and outline The Ping-Pong Evolution Hypothesis.
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Affiliation(s)
- H H Niller
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Research Center, Landshuter Str. 22, D-93047 Regensburg, Germany.
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Buzdin A, Gogvadze E, Kovalskaya E, Volchkov P, Ustyugova S, Illarionova A, Fushan A, Vinogradova T, Sverdlov E. The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. Nucleic Acids Res 2003; 31:4385-90. [PMID: 12888497 PMCID: PMC169886 DOI: 10.1093/nar/gkg496] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
L1 retrotransposons play an important role in mammalian genome shaping. In particular, they can transduce their 3'-flanking regions to new genomic loci or produce pseudogenes or retrotranscripts through reverse transcription of different kinds of cellular RNAs. Recently, we found in the human genome an unusual family of chimeric retrotranscripts composed of full-sized copies of U6 small nuclear RNAs fused at their 3' termini with 5'-truncated, 3'-poly(A)-tailed L1s. The chimeras were flanked by 11-21 bp long direct repeats, and contained near their 5' ends T2A4 hexanucleotide motifs, preferably recognized by L1 nicking endonuclease. These features suggest that the chimeras were formed using the L1 integration machinery. Here we report the identification of 81 chimeras consisting of fused DNA copies of different RNAs, including mRNAs of known human genes. Based on their structural features, the chimeras were subdivided into nine distinct families. 5' Parts of the chimeras usually originated from different nuclear RNAs, whereas their 3' parts represented cytoplasmic RNAs: mRNAs, including L1 mRNA and Alu RNA. Some of these chimeric retrotranscripts are expressed in a variety of human tissues. These findings suggest that RNA-RNA recombination during L1 reverse transcription followed by the integration of the recombinants into the host genome is a general event in genome evolution.
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Affiliation(s)
- Anton Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117871, Russia.
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Brosius J. The contribution of RNAs and retroposition to evolutionary novelties. CONTEMPORARY ISSUES IN GENETICS AND EVOLUTION 2003. [DOI: 10.1007/978-94-010-0229-5_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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