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Ricardo PC, Arias MC, de Souza Araujo N. Decoding bee cleptoparasitism through comparative transcriptomics of Coelioxoides waltheriae and its host Tetrapedia diversipes. Sci Rep 2024; 14:12361. [PMID: 38811580 PMCID: PMC11137135 DOI: 10.1038/s41598-024-56261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/04/2024] [Indexed: 05/31/2024] Open
Abstract
Cleptoparasitism, also known as brood parasitism, is a widespread strategy among bee species in which the parasite lays eggs into the nests of the host species. Even though this behavior has significant ecological implications for the dynamics of several species, little is known about the molecular pathways associated with cleptoparasitism. To shed some light on this issue, we used gene expression data to perform a comparative analysis between two solitary neotropical bees: Coelioxoides waltheriae, an obligate parasite, and their specific host Tetrapedia diversipes. We found that ortholog genes involved in signal transduction, sensory perception, learning, and memory formation were differentially expressed between the cleptoparasite and the host. We hypothesize that these genes and their associated molecular pathways are engaged in cleptoparasitism-related processes and, hence, are appealing subjects for further investigation into functional and evolutionary aspects of cleptoparasitism in bees.
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Affiliation(s)
- Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva - Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva - Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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2
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Sturm Á, Saskői É, Hotzi B, Tarnóci A, Barna J, Bodnár F, Sharma H, Kovács T, Ari E, Weinhardt N, Kerepesi C, Perczel A, Ivics Z, Vellai T. Downregulation of transposable elements extends lifespan in Caenorhabditis elegans. Nat Commun 2023; 14:5278. [PMID: 37644049 PMCID: PMC10465613 DOI: 10.1038/s41467-023-40957-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Mobility of transposable elements (TEs) frequently leads to insertional mutations in functional DNA regions. In the potentially immortal germline, TEs are effectively suppressed by the Piwi-piRNA pathway. However, in the genomes of ageing somatic cells lacking the effects of the pathway, TEs become increasingly mobile during the adult lifespan, and their activity is associated with genomic instability. Whether the progressively increasing mobilization of TEs is a cause or a consequence of ageing remains a fundamental problem in biology. Here we show that in the nematode Caenorhabditis elegans, the downregulation of active TE families extends lifespan. Ectopic activation of Piwi proteins in the soma also promotes longevity. Furthermore, DNA N6-adenine methylation at TE stretches gradually rises with age, and this epigenetic modification elevates their transcription as the animal ages. These results indicate that TEs represent a novel genetic determinant of ageing, and that N6-adenine methylation plays a pivotal role in ageing control.
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Affiliation(s)
- Ádám Sturm
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - Éva Saskői
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Bernadette Hotzi
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Anna Tarnóci
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - János Barna
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - Ferenc Bodnár
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Himani Sharma
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Tibor Kovács
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Eszter Ari
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
- HCEMM-BRC Metabolic Systems Biology Research Group, 6726, Szeged, Hungary
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári krt. 62, 6726, Szeged, Hungary
| | - Nóra Weinhardt
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI), 1111, Budapest, Hungary
- Brigham and Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - András Perczel
- Laboratory of Structural Chemistry and Biology & Hungarian Academy of Sciences (MTA)-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary.
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary.
- Vellab Biotech Ltd., 6722, Szeged, Hungary.
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Li X, Guan Z, Wang F, Wang Y, Asare E, Shi S, Lin Z, Ji T, Gao B, Song C. Evolution of piggyBac Transposons in Apoidea. INSECTS 2023; 14:402. [PMID: 37103217 PMCID: PMC10140906 DOI: 10.3390/insects14040402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
In this study, we investigated the presence of piggyBac (PB) transposons in 44 bee genomes from the Apoidea order, which is a superfamily within the Hymenoptera, which includes a large number of bee species crucial for pollination. We annotated the PB transposons in these 44 bee genomes and examined their evolution profiles, including structural characteristics, distribution, diversity, activity, and abundance. The mined PB transposons were divided into three clades, with uneven distribution in each genus of PB transposons in Apoidea. The complete PB transposons we discovered are around 2.23-3.52 kb in length and encode transposases of approximately 580 aa, with terminal inverted repeats (TIRs) of about 14 bp and 4 bp (TTAA) target-site duplications. Long TIRs (200 bp, 201 bp, and 493 bp) were also detected in some species of bees. The DDD domains of the three transposon types were more conserved, while the other protein domains were less conserved. Generally, most PB transposons showed low abundance in the genomes of Apoidea. Divergent evolution dynamics of PB were observed in the genomes of Apoidea. PB transposons in some identified species were relatively young, whiles others were older and with some either active or inactive. In addition, multiple invasions of PB were also detected in some genomes of Apoidea. Our findings highlight the contribution of PB transposons to genomic variation in these species and suggest their potential as candidates for future gene transfer tools.
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4
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Functional Characterization of the N-Terminal Disordered Region of the piggyBac Transposase. Int J Mol Sci 2022; 23:ijms231810317. [PMID: 36142241 PMCID: PMC9499001 DOI: 10.3390/ijms231810317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 09/03/2022] [Indexed: 01/15/2023] Open
Abstract
The piggyBac DNA transposon is an active element initially isolated from the cabbage looper moth, but members of this superfamily are also present in most eukaryotic evolutionary lineages. The functionally important regions of the transposase are well described. There is an RNase H-like fold containing the DDD motif responsible for the catalytic DNA cleavage and joining reactions and a C-terminal cysteine-rich domain important for interaction with the transposon DNA. However, the protein also contains a ~100 amino acid long N-terminal disordered region (NTDR) whose function is currently unknown. Here we show that deletion of the NTDR significantly impairs piggyBac transposition, although the extent of decrease is strongly cell-type specific. Moreover, replacing the NTDR with scrambled but similarly disordered sequences did not rescue transposase activity, indicating the importance of sequence conservation. Cell-based transposon excision and integration assays reveal that the excision step is more severely affected by NTDR deletion. Finally, bioinformatic analyses indicated that the NTDR is specific for the piggyBac superfamily and is also present in domesticated, transposase-derived proteins incapable of catalyzing transposition. Our results indicate an essential role of the NTDR in the “fine-tuning” of transposition and its significance in the functions of piggyBac-originated co-opted genes.
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Hammerman NM, Roff G, Lybolt T, Eyal G, Pandolfi JM. Unraveling Moreton Bay reef history: An urban high-latitude setting for coral development. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.884850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
High-latitude habitats have become increasingly recognized as a potential climate refuge for coral communities, supporting both tropical and sub-tropical corals. Despite the increasing interest in the ecology of high-latitude corals, our current knowledge of their temporal dynamics is limited, especially within urbanized settings. Here, we examined the entire history of a high-latitude coral reef ecosystem in an urbanized setting. We surveyed Holocene fossil and modern coral communities along a water quality gradient in Moreton Bay, southeast Queensland, Australia, representing near-river (Wellington Point), intermediate (Peel Island) and near-oceanic (Myora Reef) environmental conditions. Reef accretion occurred during three discrete episodes from 7,400 to 5,800, 4,900 to 3,000, and 2,100 to 300 years BP, each separated by roughly 1,000-year hiatuses, where conditions were probably not favorable enough for reef accretion to occur. Episodic reef initiation and termination suggests strong environmental controls over reef development. Eastern Australian Holocene reef growth and cessation has been linked previously to sea level fluctuations and climatic regimes (e.g., ENSO). Within each reef building episode, there were few changes in coral assemblages over time. The fast growing and branching Acropora had a relative abundance greater than 90% in ten of the 13 sediment cores and all the submerged terrace excavations. However, substantial modification of adjacent coastal catchments from European colonization in the mid 1800’s resulted in increased sediment and nutrient discharge into the bay. This perturbation coincided with a greater abundance of stress-tolerant coral species (e.g., Dipsastraea, Goniastrea, and Goniopora) and the near extirpation of Acropora in the modern coral communities of near-river and intermediate sites due to poor water quality. In contrast, the modern coral assemblage at the near-oceanic site (Myora Reef) continues to be dominated by Acropora, likely due to the consistent oceanic input, resulting in lower sediment loading and higher water quality. In order for conditions for reef growth to improve, especially within the near-river portions of the bay, further sediment and nutrient runoff from anthropogenic land-use changes need to be mitigated. Given the historical abundance of Acropora, we recommend this genus be used as an indicator of natural resource management success in the bay.
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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.
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Muller H, Loiseau V, Guillier S, Cordaux R, Gilbert C. Assessing the Impact of a Viral Infection on the Expression of Transposable Elements in the Cabbage Looper Moth (Trichoplusia ni). Genome Biol Evol 2021; 13:evab231. [PMID: 34613390 PMCID: PMC8634313 DOI: 10.1093/gbe/evab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Most studies of stress-induced transposable element (TE) expression have so far focused on abiotic sources of stress. Here, we analyzed the impact of an infection by the AcMNPV baculovirus on TE expression in a cell line (Tnms42) and midgut tissues of the cabbage looper moth (Trichoplusia ni). We find that a large fraction of TE families (576/636 in Tnms42 cells and 503/612 in midgut) is lowly expressed or not expressed at all [≤ 4 transcripts per million (TPM)] in the uninfected condition (median TPM of 0.37 in Tnms42 and 0.46 in midgut cells). In the infected condition, a total of 62 and 187 TE families were differentially expressed (DE) in midgut and Tnms42 cells, respectively, with more up- (46) than downregulated (16) TE families in the former and as many up- (91) as downregulated (96) TE families in the latter. Expression log2 fold changes of DE TE families varied from -4.95 to 9.11 in Tnms42 cells and from -4.28 to 7.66 in midgut. Large variations in expression profiles of DE TEs were observed depending on the type of cells and on time after infection. Overall, the impact of AcMNPV on TE expression in T. ni is moderate but potentially sufficient to affect TE activity and genome architecture. Interestingly, one host-derived TE integrated into AcMNPV genomes is highly expressed in infected Tnms42 cells. This result shows that virus-borne TEs can be expressed, further suggesting that they may be able to transpose and that viruses may act as vectors of horizontal transfer of TEs in insects.
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Affiliation(s)
- Héloïse Muller
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Vincent Loiseau
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Sandra Guillier
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Universite de Poitiers, CNRS, France
| | - Clément Gilbert
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
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Guérineau M, Bessa L, Moriau S, Lescop E, Bontems F, Mathy N, Guittet E, Bischerour J, Bétermier M, Morellet N. The unusual structure of the PiggyMac cysteine-rich domain reveals zinc finger diversity in PiggyBac-related transposases. Mob DNA 2021; 12:12. [PMID: 33926516 PMCID: PMC8086355 DOI: 10.1186/s13100-021-00240-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/09/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Transposons are mobile genetic elements that colonize genomes and drive their plasticity in all organisms. DNA transposon-encoded transposases bind to the ends of their cognate transposons and catalyze their movement. In some cases, exaptation of transposon genes has allowed novel cellular functions to emerge. The PiggyMac (Pgm) endonuclease of the ciliate Paramecium tetraurelia is a domesticated transposase from the PiggyBac family. It carries a core catalytic domain typical of PiggyBac-related transposases and a short cysteine-rich domain (CRD), flanked by N- and C-terminal extensions. During sexual processes Pgm catalyzes programmed genome rearrangements (PGR) that eliminate ~ 30% of germline DNA from the somatic genome at each generation. How Pgm recognizes its DNA cleavage sites in chromatin is unclear and the structure-function relationships of its different domains have remained elusive. RESULTS We provide insight into Pgm structure by determining the fold adopted by its CRD, an essential domain required for PGR. Using Nuclear Magnetic Resonance, we show that the Pgm CRD binds two Zn2+ ions and forms an unusual binuclear cross-brace zinc finger, with a circularly permutated treble-clef fold flanked by two flexible arms. The Pgm CRD structure clearly differs from that of several other PiggyBac-related transposases, among which is the well-studied PB transposase from Trichoplusia ni. Instead, the arrangement of cysteines and histidines in the primary sequence of the Pgm CRD resembles that of active transposases from piggyBac-like elements found in other species and of human PiggyBac-derived domesticated transposases. We show that, unlike the PB CRD, the Pgm CRD does not bind DNA. Instead, it interacts weakly with the N-terminus of histone H3, whatever its lysine methylation state. CONCLUSIONS The present study points to the structural diversity of the CRD among transposases from the PiggyBac family and their domesticated derivatives, and highlights the diverse interactions this domain may establish with chromatin, from sequence-specific DNA binding to contacts with histone tails. Our data suggest that the Pgm CRD fold, whose unusual arrangement of cysteines and histidines is found in all PiggyBac-related domesticated transposases from Paramecium and Tetrahymena, was already present in the ancestral active transposase that gave rise to ciliate domesticated proteins.
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Affiliation(s)
- Marc Guérineau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Luiza Bessa
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
- Present addresses: Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Séverine Moriau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Ewen Lescop
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - François Bontems
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Nathalie Mathy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
- Reproduction et Développement des Plantes UMR 5667, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon Cedex 07, France
| | - Eric Guittet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Julien Bischerour
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Mireille Bétermier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France.
| | - Nelly Morellet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 1 Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France.
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Gao B, Zong W, Miskey C, Ullah N, Diaby M, Chen C, Wang X, Ivics Z, Song C. Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals. Mob DNA 2020; 11:32. [PMID: 33303022 PMCID: PMC7731502 DOI: 10.1186/s13100-020-00227-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain largely unknown. RESULTS Here, we comprehensively investigated the evolutionary profiles of ITs, and evaluated their cut-and-paste activities in cells. ITs exhibited a narrow taxonomic distribution pattern in the animal kingdom, with invasions into two invertebrate phyla (Arthropoda and Cnidaria) and three vertebrate lineages (Actinopterygii, Agnatha, and Anura): very similar to that of the DD36E/IC family. Some animal orders and species seem to be more hospitable to Tc1/mariner transposons, one order of Amphibia and seven Actinopterygian orders are the most common orders with horizontal transfer events and have been invaded by all four families (DD38E/IT, DD35E/TR, DD36E/IC and DD37E/TRT) of Tc1/mariner transposons, and eight Actinopterygii species were identified as the major hosts of these families. Intact ITs have a total length of 1.5-1.7 kb containing a transposase gene flanked by terminal inverted repeats (TIRs). The phylogenetic tree and sequence identity showed that IT transposases were most closely related to DD34E/Tc1. ITs have been involved in multiple events of horizontal transfer in vertebrates and have invaded most lineages recently (< 5 million years ago) based on insertion age analysis. Accordingly, ITs presented high average sequence identity (86-95%) across most vertebrate species, suggesting that some are putatively active. ITs can transpose in human HeLa cells, and the transposition efficiency of consensus TIRs was higher than that of the TIRs of natural isolates. CONCLUSIONS We conclude that DD38E/IT originated from DD34E/Tc1 and can be detected in two invertebrate phyla (Arthropoda and Cnidaria), and in three vertebrate lineages (Actinopterygii, Agnatha and Anura). IT has experienced multiple HT events in animals, dominated by recent amplifications in most species and has high identity among vertebrate taxa. Our reconstructed IT transposon vector designed according to the sequence from the "cat" genome showed high cut-and-paste activity. The data suggest that IT has been acquired recently and is active in many species. This study is meaningful for understanding the evolution of the Tc1/mariner superfamily members and their hosts.
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Affiliation(s)
- Bo Gao
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China.,Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Numan Ullah
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Mohamed Diaby
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China.
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Gao B, Wang Y, Diaby M, Zong W, Shen D, Wang S, Chen C, Wang X, Song C. Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates. Mob DNA 2020; 11:25. [PMID: 32742312 PMCID: PMC7386202 DOI: 10.1186/s13100-020-00220-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Tc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family of the Tc1/mariner superfamily, are still poorly understood. RESULTS Here, phylogenetic analysis show that pogo transposases, together with Tc1/mariner, DD34E/Gambol, and Zator transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of ITm group. The pogo superfamily represents high diversity with six distinct families (Passer, Tigger, pogoR, Lemi, Mover, and Fot/Fot-like) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals-even mammals-and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix-turn-helix protein (JRK), JRK like (JRKL), pogo transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and Tigger transposable element-derived 2 to 7 (TIGD2-7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. Four genes (TIGD3, TIGD4, TIGD5, and POGZ) tend to represent ancient domestications in vertebrates, while the others only emerge in mammals and seem to be domesticated recently. Significant structural variations including target site duplication (TSD) types and the DDE triad signatures (DD29-56D) were observed for pogo transposons. Most domesticated genes are derived from the complete transposase genes; but CENPB, POGK, and POGZ are chimeric genes fused with additional functional domains. CONCLUSIONS This is the first report to systematically reveal the evolutionary profiles of the pogo transposons, suggesting that pogo and Tc1/Mariner are two separate superfamilies of ITm group, and demonstrating the repeated domestications of pogo in vertebrates. These data indicate that pogo transposons have played important roles in shaping the genome and gene evolution of fungi and animals. This study expands our understanding of the diversity of pogo transposons and updates the classification of ITm group.
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Affiliation(s)
- Bo Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yali Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Mohamed Diaby
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Wencheng Zong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Dan Shen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Saisai Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
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11
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Structural basis of seamless excision and specific targeting by piggyBac transposase. Nat Commun 2020; 11:3446. [PMID: 32651359 PMCID: PMC7351741 DOI: 10.1038/s41467-020-17128-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
The piggyBac DNA transposon is used widely in genome engineering applications. Unlike other transposons, its excision site can be precisely repaired without leaving footprints and it integrates specifically at TTAA tetranucleotides. We present cryo-EM structures of piggyBac transpososomes: a synaptic complex with hairpin DNA intermediates and a strand transfer complex capturing the integration step. The results show that the excised TTAA hairpin intermediate and the TTAA target adopt essentially identical conformations, providing a mechanistic link connecting the two unique properties of piggyBac. The transposase forms an asymmetric dimer in which the two central domains synapse the ends while two C-terminal domains form a separate dimer that contacts only one transposon end. In the strand transfer structure, target DNA is severely bent and the TTAA target is unpaired. In-cell data suggest that asymmetry promotes synaptic complex formation, and modifying ends with additional transposase binding sites stimulates activity.
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12
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Bischerour J, Bhullar S, Denby Wilkes C, Régnier V, Mathy N, Dubois E, Singh A, Swart E, Arnaiz O, Sperling L, Nowacki M, Bétermier M. Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium. eLife 2018; 7:37927. [PMID: 30223944 PMCID: PMC6143343 DOI: 10.7554/elife.37927] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/29/2018] [Indexed: 02/06/2023] Open
Abstract
The domestication of transposable elements has repeatedly occurred during evolution and domesticated transposases have often been implicated in programmed genome rearrangements, as remarkably illustrated in ciliates. In Paramecium, PiggyMac (Pgm), a domesticated PiggyBac transposase, carries out developmentally programmed DNA elimination, including the precise excision of tens of thousands of gene-interrupting germline Internal Eliminated Sequences (IESs). Here, we report the discovery of five groups of distant Pgm-like proteins (PgmLs), all able to interact with Pgm and essential for its nuclear localization and IES excision genome-wide. Unlike Pgm, PgmLs lack a conserved catalytic site, suggesting that they rather have an architectural function within a multi-component excision complex embedding Pgm. PgmL depletion can increase erroneous targeting of residual Pgm-mediated DNA cleavage, indicating that PgmLs contribute to accurately position the complex on IES ends. DNA rearrangements in Paramecium constitute a rare example of a biological process jointly managed by six distinct domesticated transposases.
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Affiliation(s)
- Julien Bischerour
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Simran Bhullar
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Institut de Biologie de l'Ecole Normale Supérieure, Paris, France
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Vinciane Régnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Univ Paris Diderot, Paris, France
| | - Nathalie Mathy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Emeline Dubois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aditi Singh
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Estienne Swart
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Mireille Bétermier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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13
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Sharma R, Nirwal S, Narayanan N, Nair DT. Dimerization through the RING-Finger Domain Attenuates Excision Activity of the piggyBac Transposase. Biochemistry 2018; 57:2913-2922. [DOI: 10.1021/acs.biochem.7b01191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rahul Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shivlee Nirwal
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Deepak T. Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
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