1
|
Bhat A, Ghatage T, Bhan S, Lahane GP, Dhar A, Kumar R, Pandita RK, Bhat KM, Ramos KS, Pandita TK. Role of Transposable Elements in Genome Stability: Implications for Health and Disease. Int J Mol Sci 2022; 23:7802. [PMID: 35887150 PMCID: PMC9319628 DOI: 10.3390/ijms23147802] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.
Collapse
Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Trupti Ghatage
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Ganesh P. Lahane
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Arti Dhar
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra 182320, India;
| | - Raj K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| | - Tej K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| |
Collapse
|
2
|
Palazzo A, Caizzi R, Moschetti R, Marsano RM. What Have We Learned in 30 Years of Investigations on Bari Transposons? Cells 2022; 11:583. [PMID: 35159391 PMCID: PMC8834629 DOI: 10.3390/cells11030583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) have been historically depicted as detrimental genetic entities that selfishly aim at perpetuating themselves, invading genomes, and destroying genes. Scientists often co-opt "special" TEs to develop new and powerful genetic tools, that will hopefully aid in changing the future of the human being. However, many TEs are gentle, rarely unleash themselves to harm the genome, and bashfully contribute to generating diversity and novelty in the genomes they have colonized, yet they offer the opportunity to develop new molecular tools. In this review we summarize 30 years of research focused on the Bari transposons. Bari is a "normal" transposon family that has colonized the genomes of several Drosophila species and introduced genomic novelties in the melanogaster species. We discuss how these results have contributed to advance the field of TE research and what future studies can still add to the current knowledge.
Collapse
|
3
|
Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes. Cells 2021; 10:cells10123590. [PMID: 34944100 PMCID: PMC8700633 DOI: 10.3390/cells10123590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.
Collapse
|
4
|
Berloco MF, Minervini CF, Moschetti R, Palazzo A, Viggiano L, Marsano RM. Evidence of the Physical Interaction between Rpl22 and the Transposable Element Doc5, a Heterochromatic Transposon of Drosophila melanogaster. Genes (Basel) 2021; 12:1997. [PMID: 34946947 PMCID: PMC8701128 DOI: 10.3390/genes12121997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/06/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022] Open
Abstract
Chromatin is a highly dynamic biological entity that allows for both the control of gene expression and the stabilization of chromosomal domains. Given the high degree of plasticity observed in model and non-model organisms, it is not surprising that new chromatin components are frequently described. In this work, we tested the hypothesis that the remnants of the Doc5 transposable element, which retains a heterochromatin insertion pattern in the melanogaster species complex, can be bound by chromatin proteins, and thus be involved in the organization of heterochromatic domains. Using the Yeast One Hybrid approach, we found Rpl22 as a potential interacting protein of Doc5. We further tested in vitro the observed interaction through Electrophoretic Mobility Shift Assay, uncovering that the N-terminal portion of the protein is sufficient to interact with Doc5. However, in situ localization of the native protein failed to detect Rpl22 association with chromatin. The results obtained are discussed in the light of the current knowledge on the extra-ribosomal role of ribosomal protein in eukaryotes, which suggests a possible role of Rpl22 in the determination of the heterochromatin in Drosophila.
Collapse
Affiliation(s)
- Maria Francesca Berloco
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Crescenzio Francesco Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Roberta Moschetti
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Antonio Palazzo
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Luigi Viggiano
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | | |
Collapse
|
5
|
Specchia V, Bozzetti MP. The Role of HSP90 in Preserving the Integrity of Genomes Against Transposons Is Evolutionarily Conserved. Cells 2021; 10:cells10051096. [PMID: 34064379 PMCID: PMC8147803 DOI: 10.3390/cells10051096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/31/2022] Open
Abstract
The HSP90 protein is a molecular chaperone intensively studied for its role in numerous cellular processes both under physiological and stress conditions. This protein acts on a wide range of substrates with a well-established role in cancer and neurological disorders. In this review, we focused on the involvement of HSP90 in the silencing of transposable elements and in the genomic integrity maintenance. The common feature of transposable elements is the potential jumping in new genomic positions, causing chromosome structure rearrangements, gene mutations, and influencing gene expression levels. The role of HSP90 in the control of these elements is evolutionarily conserved and opens new perspectives in the HSP90-related mechanisms underlying human disorders. Here, we discuss the hypothesis that its role in the piRNA pathway regulating transposons may be implicated in the onset of neurological diseases.
Collapse
|
6
|
Palazzo A, Marsano RM. Transposable elements: a jump toward the future of expression vectors. Crit Rev Biotechnol 2021; 41:792-808. [PMID: 33622117 DOI: 10.1080/07388551.2021.1888067] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Expression vectors (EVs) are artificial nucleic acid molecules with a modular structure that allows for the transcription of DNA sequences of interest in either cellular or cell-free environments. These vectors have emerged as cross-disciplinary tools with multiple applications in an expanding Life Sciences market. The cis-regulatory sequences (CRSs) that control the transcription in EVs are typically sourced from either viruses or from characterized genes. However, the recent advancement in transposable elements (TEs) technology provides attractive alternatives that may enable a significant improvement in the design of EVs. Commonly known as "jumping genes," due to their ability to move between genetic loci, TEs are constitutive components of both eukaryotic and prokaryotic genomes. TEs harbor native CRSs that allow the regulated transcription of transposition-related genes. However, some TE-related CRSs display striking characteristics, which provides the opportunity to reconsider TEs as lead actors in the design of EVs. In this article, we provide a synopsis of the transcriptional control elements commonly found in EVs together with an extensive discussion of their advantages and limitations. We also highlight the latest findings that may allow for the implementation of TE-derived sequences in the EVs feasible, possibly improving existing vectors. By introducing this new concept of TEs as a source of regulatory sequences, we aim to stimulate a profitable discussion of the potential advantages and benefits of developing a new generation of EVs based on the use of TE-derived control sequences.
Collapse
Affiliation(s)
- Antonio Palazzo
- Laboratory of Translational Nanotechnology, "Istituto Tumori Giovanni Paolo II" I.R.C.C.S, Bari, Italy
| | | |
Collapse
|
7
|
Palazzo A, Escuder E, D'Addabbo P, Lovero D, Marsano RM. A genomic survey of Tc1-mariner transposons in nematodes suggests extensive horizontal transposon transfer events. Mol Phylogenet Evol 2021; 158:107090. [PMID: 33545274 DOI: 10.1016/j.ympev.2021.107090] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 01/24/2023]
Abstract
The number of reports concerning horizontal transposon transfers (HTT) in metazoan species is considerably increased, alongside with the exponential growth of genomic sequence data However, our understanding of the mechanisms of such phenomenon is still at an early stage. Nematodes constitute an animal phylum successfully adapted to almost every ecosystem and for this reason could potentially contribute to spreading the genetic information through horizontal transfer. To date, few studies describe HTT of nematode retrotransposons. This is due to the lack of annotation of transposable elements in the sequenced nematode genomes, especially DNA transposons, which are acknowledged as the best horizontal travelers among mobile sequences. We have therefore started a survey of DNA transposons and their possible involvement in HTT in sequenced nematode genomes. Here, we describe 83 new Tc1/mariner elements distributed in 17 nematode species. Among them, nine families were possibly horizontally transferred between nematodes and the most diverse animal species, including ants as preferred partner of HTT. The results obtained suggest that HTT events involving nematodes Tc1/mariner elements are not uncommon, and that nematodes could have a possible role as transposon reservoir that, in turn, can be redistributed among animal genomes. Overall, this could be relevant to understand how the inter-species genetic flows shape the landscape of genetic variation of organisms inhabiting specific environmental communities.
Collapse
Affiliation(s)
- Antonio Palazzo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Elsa Escuder
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Pietro D'Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Domenica Lovero
- Dipartimento di Scienze Biomediche ed Oncologia Umana (DIMO), Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | | |
Collapse
|
8
|
Moschetti R, Palazzo A, Lorusso P, Viggiano L, Massimiliano Marsano R. "What You Need, Baby, I Got It": Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila. BIOLOGY 2020; 9:E25. [PMID: 32028630 PMCID: PMC7168160 DOI: 10.3390/biology9020025] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022]
Abstract
Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome's structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE-host interactions in any complex eukaryotic genome.
Collapse
Affiliation(s)
- Roberta Moschetti
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - Antonio Palazzo
- Laboratory of Translational Nanotechnology, “Istituto Tumori Giovanni Paolo II” I.R.C.C.S, Viale Orazio Flacco 65, 70125 Bari, Italy;
| | - Patrizio Lorusso
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - Luigi Viggiano
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - René Massimiliano Marsano
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| |
Collapse
|
9
|
Palazzo A, Lorusso P, Miskey C, Walisko O, Gerbino A, Marobbio CMT, Ivics Z, Marsano RM. Transcriptionally promiscuous "blurry" promoters in Tc1/ mariner transposons allow transcription in distantly related genomes. Mob DNA 2019; 10:13. [PMID: 30988701 PMCID: PMC6446368 DOI: 10.1186/s13100-019-0155-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/26/2019] [Indexed: 12/04/2022] Open
Abstract
Background We have recently described a peculiar feature of the promoters in two Drosophila Tc1-like elements, Bari1 and Bari3. The AT-richness and the presence of weak core-promoter motifs make these promoters, that we have defined “blurry”, able to activate transcription of a reporter gene in cellular systems as diverse as fly, human, yeast and bacteria. In order to clarify whether the blurry promoter is a specific feature of the Bari transposon family, we have extended this study to promoters isolated from three additional DNA transposon and from two additional LTR retrotransposons. Results Here we show that the blurry promoter is also a feature of two vertebrate transposable elements, Sleeping Beauty and Hsmar1, belonging to the Tc1/mariner superfamily. In contrast, this feature is not shared by the promoter of the hobo transposon, which belongs to the hAT superfamily, nor by LTR retrotransposon-derived promoters, which, in general, do not activate transcription when introduced into non-related genomes. Conclusions Our results suggest that the blurry promoter could be a shared feature of the members of the Tc1/mariner superfamily with possible evolutionary and biotechnological implications. Electronic supplementary material The online version of this article (10.1186/s13100-019-0155-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Antonio Palazzo
- 1Department of Biology, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy.,Present address: Laboratory of Translational Nanotechnology, "Istituto Tumori Giovanni Paolo II" I.R.C.C.S, Viale Orazio Flacco 65, 70125 Bari, Italy
| | - Patrizio Lorusso
- 1Department of Biology, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
| | - Csaba Miskey
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Oliver Walisko
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Andrea Gerbino
- 3Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | | | - Zoltán Ivics
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | | |
Collapse
|
10
|
Palazzo A, Caizzi R, Viggiano L, Marsano RM. Does the Promoter Constitute a Barrier in the Horizontal Transposon Transfer Process? Insight from Bari Transposons. Genome Biol Evol 2018; 9:1637-1645. [PMID: 28854630 PMCID: PMC5570127 DOI: 10.1093/gbe/evx122] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2017] [Indexed: 12/11/2022] Open
Abstract
The contribution of the transposons’ promoter in the horizontal transfer process is quite overlooked in the scientific literature. To shed light on this aspect we have mimicked the horizontal transfer process in laboratory and assayed in a wide range of hosts (fly, human, yeast and bacteria) the promoter activity of the 5′ terminal sequences in Bari1 and Bari3, two Drosophila transposons belonging to the Tc1-mariner superfamily. These sequences are able to drive the transcription of a reporter gene even in distantly related organisms at least at the episomal level. By combining bioinformatics and experimental approaches, we define two distinct promoter sequences for each terminal sequence analyzed, which allow transcriptional activity in prokaryotes and eukaryotes, respectively. We propose that the Bari family of transposons, and possibly other members of the Tc1-mariner superfamily, might have evolved “blurry promoters,” which have facilitated their diffusion in many living organisms through horizontal transfer.
Collapse
Affiliation(s)
- Antonio Palazzo
- Department of Biology, University of Bari "Aldo Moro," Italy
| | - Ruggiero Caizzi
- Department of Biology, University of Bari "Aldo Moro," Italy
| | - Luigi Viggiano
- Department of Biology, University of Bari "Aldo Moro," Italy
| | | |
Collapse
|
11
|
Specchia V, D'Attis S, Puricella A, Bozzetti MP. dFmr1 Plays Roles in Small RNA Pathways of Drosophila melanogaster. Int J Mol Sci 2017; 18:ijms18051066. [PMID: 28509881 PMCID: PMC5454977 DOI: 10.3390/ijms18051066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 11/16/2022] Open
Abstract
Fragile-X syndrome is the most common form of inherited mental retardation accompanied by other phenotypes, including macroorchidism. The disorder originates with mutations in the Fmr1 gene coding for the FMRP protein, which, with its paralogs FXR1 and FXR2, constitute a well-conserved family of RNA-binding proteins. Drosophila melanogaster is a good model for the syndrome because it has a unique fragile X-related gene: dFmr1. Recently, in addition to its confirmed role in the miRNA pathway, a function for dFmr1 in the piRNA pathway, operating in Drosophila gonads, has been established. In this review we report a summary of the piRNA pathways occurring in gonads with a special emphasis on the relationship between the piRNA genes and the crystal-Stellate system; we also analyze the roles of dFmr1 in the Drosophila gonads, exploring their genetic and biochemical interactions to reveal some unexpected connections.
Collapse
Affiliation(s)
- Valeria Specchia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA)-University of Salento, 73100 Lecce, Italy.
| | - Simona D'Attis
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA)-University of Salento, 73100 Lecce, Italy.
| | - Antonietta Puricella
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA)-University of Salento, 73100 Lecce, Italy.
| | - Maria Pia Bozzetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA)-University of Salento, 73100 Lecce, Italy.
| |
Collapse
|
12
|
McCullers TJ, Steiniger M. Transposable elements in Drosophila. Mob Genet Elements 2017; 7:1-18. [PMID: 28580197 PMCID: PMC5443660 DOI: 10.1080/2159256x.2017.1318201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster.
Collapse
Affiliation(s)
| | - Mindy Steiniger
- Department of Biology, University of Missouri, St. Louis, MO, USA
| |
Collapse
|
13
|
Palazzo A, Lovero D, D’Addabbo P, Caizzi R, Marsano RM. Identification of Bari Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer. PLoS One 2016; 11:e0156014. [PMID: 27213270 PMCID: PMC4877112 DOI: 10.1371/journal.pone.0156014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/09/2016] [Indexed: 11/18/2022] Open
Abstract
Bari elements are members of the Tc1-mariner superfamily of DNA transposons, originally discovered in Drosophila melanogaster, and subsequently identified in silico in 11 sequenced Drosophila genomes and as experimentally isolated in four non-sequenced Drosophila species. Bari-like elements have been also studied for their mobility both in vivo and in vitro. We analyzed 23 Drosophila genomes and carried out a detailed characterization of the Bari elements identified, including those from the heterochromatic Bari1 cluster in D. melanogaster. We have annotated 401 copies of Bari elements classified either as putatively autonomous or inactive according to the structure of the terminal sequences and the presence of a complete transposase-coding region. Analyses of the integration sites revealed that Bari transposase prefers AT-rich sequences in which the TA target is cleaved and duplicated. Furthermore evaluation of transposon’s co-occurrence near the integration sites of Bari elements showed a non-random distribution of other transposable elements. We also unveil the existence of a putatively autonomous Bari1 variant characterized by two identical long Terminal Inverted Repeats, in D. rhopaloa. In addition, we detected MITEs related to Bari transposons in 9 species. Phylogenetic analyses based on transposase gene and the terminal sequences confirmed that Bari-like elements are distributed into three subfamilies. A few inconsistencies in Bari phylogenetic tree with respect to the Drosophila species tree could be explained by the occurrence of horizontal transfer events as also suggested by the results of dS analyses. This study further clarifies the Bari transposon’s evolutionary dynamics and increases our understanding on the Tc1-mariner elements’ biology.
Collapse
Affiliation(s)
- Antonio Palazzo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro” via Orabona 4 70125, Bari, Italy
| | - Domenica Lovero
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Via Amendola 165/A, 70126, Bari, Italy
| | - Pietro D’Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro” via Orabona 4 70125, Bari, Italy
| | - Ruggiero Caizzi
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro” via Orabona 4 70125, Bari, Italy
| | - René Massimiliano Marsano
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro” via Orabona 4 70125, Bari, Italy
- * E-mail:
| |
Collapse
|
14
|
Palazzo A, Moschetti R, Caizzi R, Marsano RM. The Drosophila mojavensis Bari3 transposon: distribution and functional characterization. Mob DNA 2014; 5:21. [PMID: 25093043 PMCID: PMC4120734 DOI: 10.1186/1759-8753-5-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/13/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Bari-like transposons belong to the Tc1-mariner superfamily, and they have been identified in several genomes of the Drosophila genus. This transposon's family has been used as paradigm to investigate the complex dynamics underlying the persistence and structural evolution of transposable elements (TEs) within a genome. Three structural Bari variants have been identified so far and can be distinguished based on the organization of their terminal inverted repeats. Bari3 is the last discovered member of this family identified in Drosophila mojavensis, a recently emerged species of the Repleta group of the genus Drosophila. RESULTS We studied the insertion pattern of Bari3 in different D. mojavensis populations and found evidence of recent transposition activity. Analysis of the transposase domains unveiled the presence of a functional nuclear localization signal, as well as a functional binding domain. Using luciferase-based assays, we investigated the promoter activity of Bari3 as well as the interaction of its transposase with its left terminus. The results suggest that Bari3 is transposition-competent. Finally we demonstrated transposase transcript processing when the transposase gene is overexpressed in vivo and in vitro. CONCLUSIONS Bari3 displays very similar structural and functional features with its close relative, Bari1. Our results strongly suggest that Bari3 is an independent element that has generated genomic diversity in D. mojavensis. It can autonomously transcribe its transposase gene, which in turn can localize in the nucleus and bind the terminal inverted repeats of the transposon. Nevertheless, the identification of an unpredicted spliced form of the Bari3 transposase transcript allows us to hypothesize a control mechanism of its mobility based on mRNA processing. These results will aid the studies on the Bari family of transposons, which is intriguing for its widespread diffusion in Drosophilids coupled with a structural diversity generated during the evolution of Bari-like elements in their host genomes.
Collapse
Affiliation(s)
- Antonio Palazzo
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - Roberta Moschetti
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - Ruggiero Caizzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - René Massimiliano Marsano
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| |
Collapse
|