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Luo S, Li A, Luo J, Liao G, Li X, Yao S, Wang A, Xiao D, He L, Zhan J. Mutator-like transposable element 9A interacts with metacaspase 1 and modulates the incidence of Al-induced programmed cell death in peanut. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2113-2126. [PMID: 38069635 DOI: 10.1093/jxb/erad489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/05/2023] [Indexed: 03/28/2024]
Abstract
The toxicity of aluminum (Al) in acidic soil inhibits plant root development and reduces crop yields. In the plant response to Al toxicity, the initiation of programmed cell death (PCD) appears to be an important mechanism for the elimination of Al-damaged cells to ensure plant survival. In a previous study, the type I metacaspase AhMC1 was found to regulate the Al stress response and to be essential for Al-induced PCD. However, the mechanism by which AhMC1 is altered in the peanut response to Al stress remained unclear. Here, we show that a nuclear protein, mutator-like transposable element 9A (AhMULE9A), directly interacts with AhMC1 in vitro and in vivo. This interaction occurs in the nucleus in peanut and is weakened during Al stress. Furthermore, a conserved C2HC zinc finger domain of AhMULE9A (residues 735-751) was shown to be required for its interaction with AhMC1. Overexpression of AhMULE9A in Arabidopsis and peanut strongly inhibited root growth with a loss of root cell viability under Al treatment. Conversely, knock down of AhMULE9A in peanut significantly reduced Al uptake and Al inhibition of root growth, and alleviated the occurrence of typical hallmarks of Al-induced PCD. These findings provide novel insight into the regulation of Al-induced PCD.
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Affiliation(s)
- Shuzhen Luo
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ailing Li
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jin Luo
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Guoting Liao
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Xia Li
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Shaochang Yao
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, 530200, China
| | - Aiqin Wang
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Dong Xiao
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Longfei He
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jie Zhan
- College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
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Hunter CT, McCarty DR, Koch KE. Independent evolution of transposase and TIRs facilitated by recombination between Mutator transposons from divergent clades in maize. Proc Natl Acad Sci U S A 2023; 120:e2305298120. [PMID: 37490540 PMCID: PMC10401008 DOI: 10.1073/pnas.2305298120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 07/27/2023] Open
Abstract
Nearly all eukaryotes carry DNA transposons of the Robertson's Mutator (Mu) superfamily, a widespread source of genome instability and genetic variation. Despite their pervasive impact on host genomes, much remains unknown about the evolution of these transposons. Transposase recognition of terminal inverted repeats (TIRs) is thought to drive and constrain coevolution of MuDR transposase genes and TIRs. To address the extent of this relationship and its impact, we compared separate phylogenies of TIRs and MuDR gene sequences from Mu elements in the maize genome. Five major clades were identified. As expected, most Mu elements were bound by highly similar TIRs from the same clade (homomorphic type). However, a subset of elements contained dissimilar TIRs derived from divergent clades. These "heteromorphs" typically occurred in multiple copies indicating active transposition in the genome. In addition, analysis of internal sequences showed that exchanges between elements having divergent TIRs produced new mudra and mudrb gene combinations. In several instances, TIR homomorphs had been regenerated within a heteromorph clade with retention of distinctive internal MuDR sequence combinations. Results reveal that recombination between divergent clades facilitates independent evolution of transposase (mudra), transposase-binding targets (TIRs), and capacity for insertion (mudrb) of active Mu elements. This mechanism would be enhanced by the preference of Mu insertions for recombination-rich regions near the 5' ends of genes. We suggest that cycles of recombination give rise to alternating homo- and heteromorph forms that enhance the diversity on which selection for Mu fitness can operate.
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Affiliation(s)
- Charles T. Hunter
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, United States Department of Agriculture - Agricultural Research Service, Gainesville, FL32608
| | - Donald R. McCarty
- Horticultural Sciences Department, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL32611
| | - Karen E. Koch
- Horticultural Sciences Department, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL32611
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Mukherjee K, Moroz LL. Transposon-derived transcription factors across metazoans. Front Cell Dev Biol 2023; 11:1113046. [PMID: 36960413 PMCID: PMC10027918 DOI: 10.3389/fcell.2023.1113046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
Transposable elements (TE) could serve as sources of new transcription factors (TFs) in plants and some other model species, but such evidence is lacking for most animal lineages. Here, we discovered multiple independent co-options of TEs to generate 788 TFs across Metazoa, including all early-branching animal lineages. Six of ten superfamilies of DNA transposon-derived conserved TF families (ZBED, CENPB, FHY3, HTH-Psq, THAP, and FLYWCH) were identified across nine phyla encompassing the entire metazoan phylogeny. The most extensive convergent domestication of potentially TE-derived TFs occurred in the hydroid polyps, polychaete worms, cephalopods, oysters, and sea slugs. Phylogenetic reconstructions showed species-specific clustering and lineage-specific expansion; none of the identified TE-derived TFs revealed homologs in their closest neighbors. Together, our study established a framework for categorizing TE-derived TFs and informing the origins of novel genes across phyla.
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Affiliation(s)
- Krishanu Mukherjee
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
- *Correspondence: Leonid L. Moroz, ; Krishanu Mukherjee,
| | - Leonid L. Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
- Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, United States
- *Correspondence: Leonid L. Moroz, ; Krishanu Mukherjee,
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Cloning of Maize TED Transposon into Escherichia coli Reveals the Polychromatic Sequence Landscape of Refractorily Propagated Plasmids. Int J Mol Sci 2022; 23:ijms231911993. [PMID: 36233292 PMCID: PMC9569675 DOI: 10.3390/ijms231911993] [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: 08/30/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
MuDR, the founder member of the Mutator superfamily and its MURA transcripts, has been identified as toxic sequences to Escherichia coli (E. coli), which heavily hindered the elucidation of the biochemical features of MURA transposase and confined the broader application of the Mutator system in other organisms. To harness less constrained systems as alternatives, we attempted to clone TED and Jittery, two recently isolated autonomous Mutator-like elements (MULEs) from maize, respectively. Their full-length transcripts and genomic copies are successfully cloned when the incubation time for bacteria to recover from heat shock is extended appropriately prior to plating. However, during their proliferation in E. coli, TED transformed plasmids are unstable, as evidenced by derivatives from which frameshift, deletion mutations, or IS transposon insertions are readily detected. Our results suggest that neither leaky expression of the transposase nor the presence of terminal inverse repeats (TIRs) are responsible for the cloning barriers, which were once ascribed to the presence of the Shine–Dalgarno-like sequence. Instead, the internal sequence of TED (from 1250 to 2845 bp), especially the exons in this region, was the most likely causer. The findings provide novel insights into the property and function of the Mutator superfamily and shed light on the dissection of toxic effects on cloning from MULEs.
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Gao D, Caspersen AM, Hu G, Bockelman HE, Chen X. A Novel Mutator-Like Transposable Elements With Unusual Structure and Recent Transpositions in Barley ( Hordeum vulgare). FRONTIERS IN PLANT SCIENCE 2022; 13:904619. [PMID: 35677233 PMCID: PMC9168764 DOI: 10.3389/fpls.2022.904619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Mutator-like transposable elements (MULEs) represent a unique superfamily of DNA transposons as they can capture host genes and cause higher frequency of mutations in some eukaryotes. Despite their essential roles in plant evolution and functional genomics, MULEs are not fully understood yet in many important crops including barley (Hordeum vulgare). In this study, we analyzed the barley genome and identified a new mutator transposon Hvu_Abermu. This transposon is present at extremely high copy number in barley and shows unusual structure as it contains three open reading frames (ORFs) including one ORF (ORF1) encoding mutator transposase protein and one ORF (ORFR) showing opposite transcriptional orientation. We identified homologous sequences of Hvu_Abermu in both monocots and dicots and grouped them into a large mutator family named Abermu. Abermu transposons from different species share significant sequence identity, but they exhibit distinct sequence structures. Unlike the transposase proteins which are highly conserved between Abermu transposons from different organisms, the ORFR-encoded proteins are quite different from distant species. Phylogenetic analysis indicated that Abermu transposons shared closer evolutionary relationships with the maize MuDR transposon than other reported MULEs. We also found phylogenetic incongruence for the Abermu transposons identified in rice and its wild species implying the possibility of horizontal transfer of transposon. Further comparison indicated that over 200 barley genes contain Abermu-related sequences. We analyzed the barley pan genomes and detected polymorphic Hvu_Abermu transposons between the sequenced 23 wild and cultivated barley genomes. Our efforts identified a novel mutator transposon and revealed its recent transposition activity, which may help to develop genetic tools for barley and other crops.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States
| | - Ann M. Caspersen
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States
| | - Gongshe Hu
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States
| | - Harold E. Bockelman
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, United States
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, United States
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Liu Z, An C, Zhao Y, Xiao Y, Bao L, Gong C, Gao Y. Genome-Wide Identification and Characterization of the CsFHY3/FAR1 Gene Family and Expression Analysis under Biotic and Abiotic Stresses in Tea Plants ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10030570. [PMID: 33802900 PMCID: PMC8002597 DOI: 10.3390/plants10030570] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 05/17/2023]
Abstract
The FHY3/FAR1 transcription factor family, derived from transposases, plays important roles in light signal transduction, and in the growth and development of plants. However, the homologous genes in tea plants have not been studied. In this study, 25 CsFHY3/FAR1 genes were identified in the tea plant genome through a genome-wide study, and were classified into five subgroups based on their phylogenic relationships. Their potential regulatory roles in light signal transduction and photomorphogenesis, plant growth and development, and hormone responses were verified by the existence of the corresponding cis-acting elements. The transcriptome data showed that these genes could respond to salt stress and shading treatment. An expression analysis revealed that, in different tissues, especially in leaves, CsFHY3/FAR1s were strongly expressed, and most of these genes were positively expressed under salt stress (NaCl), and negatively expressed under low temperature (4 °C) stress. In addition, a potential interaction network demonstrated that PHYA, PHYC, PHYE, LHY, FHL, HY5, and other FRSs were directly or indirectly associated with CsFHY3/FAR1 members. These results will provide the foundation for functional studies of the CsFHY3/FAR1 family, and will contribute to the breeding of tea varieties with high light efficiency and strong stress resistance.
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Affiliation(s)
- Zhengjun Liu
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
| | - Chuanjing An
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China;
| | - Yiqing Zhao
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
| | - Yao Xiao
- Department of Foreign Languages, Northwest A&F University, Xianyang 712100, China;
| | - Lu Bao
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
| | - Chunmei Gong
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
| | - Yuefang Gao
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
- Correspondence: ; Tel.: +86-029-8708-2613
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7
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Tang Y, Ma X, Zhao S, Xue W, Zheng X, Sun H, Gu P, Zhu Z, Sun C, Liu F, Tan L. Identification of an active miniature inverted-repeat transposable element mJing in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:639-653. [PMID: 30689248 PMCID: PMC6850418 DOI: 10.1111/tpj.14260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/01/2019] [Accepted: 01/18/2019] [Indexed: 05/27/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are structurally homogeneous non-autonomous DNA transposons with high copy numbers that play important roles in genome evolution and diversification. Here, we analyzed the rice high-tillering dwarf (htd) mutant in an advanced backcross population between cultivated and wild rice, and identified an active MITE named miniature Jing (mJing). The mJing element belongs to the PIF/Harbinger superfamily. japonica rice var. Nipponbare and indica var. 93-11 harbor 72 and 79 mJing family members, respectively, have undergone multiple rounds of amplification bursts during the evolution of Asian cultivated rice (Oryza sativa L.). A heterologous transposition experiment in Arabidopsis thaliana indicated that the autonomous element Jing is likely to have provides the transposase needed for mJing mobilization. We identified 297 mJing insertion sites and their presence/absence polymorphism among 71 rice samples through targeted high-throughput sequencing. The results showed that the copy number of mJing varies dramatically among Asian cultivated rice (O. sativa), its wild ancestor (O. rufipogon), and African cultivated rice (O. glaberrima) and that some mJing insertions are subject to directional selection. These findings suggest that the amplification and removal of mJing elements have played an important role in rice genome evolution and species diversification.
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Affiliation(s)
- Yanyan Tang
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xin Ma
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Shuangshuang Zhao
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Wei Xue
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xu Zheng
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Hongying Sun
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Ping Gu
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Zuofeng Zhu
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Lubin Tan
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
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Dupeyron M, Singh KS, Bass C, Hayward A. Evolution of Mutator transposable elements across eukaryotic diversity. Mob DNA 2019; 10:12. [PMID: 30988700 PMCID: PMC6446971 DOI: 10.1186/s13100-019-0153-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/01/2019] [Indexed: 11/15/2022] Open
Abstract
Background Mutator-like elements (MULEs) are a significant superfamily of DNA transposons on account of their: (i) great transpositional activity and propensity for insertion in or near gene sequences, (ii) their consequent high mutagenic capacity, and, (iii) their tendency to acquire host gene fragments. Consequently, MULEs are important genetic tools and represent a key study system for research into host-transposon interactions. Yet, while several studies have focused on the impacts of MULEs on crop and fungus genomes, their evolution remains poorly explored. Results We perform comprehensive bioinformatic and phylogenetic analyses to address currently available MULE diversity and reconstruct evolution for the group. For this, we mine MULEs from online databases, and combine search results with available transposase sequences retrieved from previously published studies. Our analyses uncover two entirely new MULE clades that contain elements almost entirely restricted to arthropod hosts, considerably expanding the set of MULEs known from this group, suggesting that many additional MULEs may await discovery from further arthropod genomes. In several cases, close relationships occur between MULEs recovered from distantly related host organisms, suggesting that horizontal transfer events may have played an important role in the evolution of the group. However, it is apparent that MULEs from plants remain separate from MULEs identified from other host groups. MULE structure varies considerably across phylogeny, and TIR length is shown to vary greatly both within and between MULE groups. Our phylogeny suggests that MULE diversity is clustered in well-supported groups, typically according to host taxonomy. With reference to this, we make suggestions on how MULE diversity can be partitioned to provide a robust taxonomic framework. Conclusions Our study represents a considerable advance in the understanding of MULE diversity, host range and evolution, and provides a taxonomic framework for the classification of further MULE elements that await discovery. Our findings also raise a number of questions relating to MULE biology, suggesting that this group will provide a rich avenue for future study. Electronic supplementary material The online version of this article (10.1186/s13100-019-0153-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mathilde Dupeyron
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Kumar S Singh
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
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Battilana J, Dunlevy JD, Boss PK. Histone modifications at the grapevine VvOMT3 locus, which encodes an enzyme responsible for methoxypyrazine production in the berry. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:655-664. [PMID: 32480596 DOI: 10.1071/fp16434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/16/2017] [Indexed: 05/21/2023]
Abstract
Some herbaceous characters in wine are attributed to the presence of aroma compounds collectively known as methoxypyrazines (MPs). In grape berries their formation has been hypothesised to start from a reaction of two amino acids or an amino acid and an unknown 1,2-dicarbonyl compound, leading to the formation of hydroxypyrazine, which is then enzymatically methylated to form a MP. The enzyme responsible of the formation of 3-isobutyl-2-methoxypyrazine has been recently identified as VvOMT3 whose regulation is still not understood. The concentration of MPs in grapes is known to be influenced by development, environmental stimuli and most importantly grape variety. In order to investigate the chromatin arrangement of that region a chromatin immunoprecipitation analysis has been performed and putative differences in epigenetic regulation of VvOMT3 spatially between the skin and flesh tissues and also temporally during fruit development have been detected. There are also allelic differences in VvOMT3 histone modifications which are maintained in subsequent generations. This study provides evidence of histone tail modification of the VvOMT3 locus in grapevine, which may play a role in the spatial and developmental regulation of the expression of this gene.
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Affiliation(s)
- Juri Battilana
- FEM-IASMA Genomics and Biology of Fruit Crop Department, Research and Innovation Centre - Fondazione Edmund Mach. Via E. Mach 1, 38010 - S. Michele all'Adige (TN), Italy
| | - Jake D Dunlevy
- CSIRO Agriculture and Food, PMB 2, Glen Osmond, SA 5064, Australia
| | - Paul K Boss
- CSIRO Agriculture and Food, PMB 2, Glen Osmond, SA 5064, Australia
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10
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Liu K, Wessler SR. Functional characterization of the active Mutator-like transposable element, Muta1 from the mosquito Aedes aegypti. Mob DNA 2017; 8:1. [PMID: 28096902 PMCID: PMC5225508 DOI: 10.1186/s13100-016-0084-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/19/2016] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Mutator-like transposable elements (MULEs) are widespread with members in fungi, plants, and animals. Most of the research on the MULE superfamily has focused on plant MULEs where they were discovered and where some are extremely active and have significant impact on genome structure. The maize MuDR element has been widely used as a tool for both forward and reverse genetic studies because of its high transposition rate and preference for targeting genic regions. However, despite being widespread, only a few active MULEs have been identified, and only one, the rice Os3378, has demonstrated activity in a non-host organism. RESULTS Here we report the identification of potentially active MULEs in the mosquito Aedes aegypti. We demonstrate that one of these, Muta1, is capable of excision and reinsertion in a yeast transposition assay. Element reinsertion generated either 8 bp or 9 bp target site duplications (TSDs) with no apparent sequence preference. Mutagenesis analysis of donor site TSDs in the yeast assay indicates that their presence is important for precise excision and enhanced transposition. Site directed mutagenesis of the putative DDE catalytic motif and other conserved residues in the transposase protein abolished transposition activity. CONCLUSIONS Collectively, our data indicates that the Muta1 transposase of Ae. aegypti can efficiently catalyze both excision and reinsertion reactions in yeast. Mutagenesis analysis reveals that several conserved amino acids, including the DDE triad, play important roles in transposase function. In addition, donor site TSD also impacts the transposition of Muta1.
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Affiliation(s)
- Kun Liu
- Graduate Program in Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Susan R Wessler
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
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11
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Abstract
The Mutator system of transposable elements (TEs) is a highly mutagenic family of transposons in maize. Because they transpose at high rates and target genic regions, these transposons can rapidly generate large numbers of new mutants, which has made the Mutator system a favored tool for both forward and reverse mutagenesis in maize. Low copy number versions of this system have also proved to be excellent models for understanding the regulation and behavior of Class II transposons in plants. Notably, the availability of a naturally occurring locus that can heritably silence autonomous Mutator elements has provided insights into the means by which otherwise active transposons are recognized and silenced. This chapter will provide a review of the biology, regulation, evolution and uses of this remarkable transposon system, with an emphasis on recent developments in our understanding of the ways in which this TE system is recognized and epigenetically silenced as well as recent evidence that Mu-like elements (MULEs) have had a significant impact on the evolution of plant genomes.
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12
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MuTAnT: a family of Mutator-like transposable elements targeting TA microsatellites in Medicago truncatula. Genetica 2015; 143:433-40. [PMID: 25981486 PMCID: PMC4486113 DOI: 10.1007/s10709-015-9842-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/10/2015] [Indexed: 12/31/2022]
Abstract
Transposable elements (TEs) are mobile DNA segments, abundant and dynamic in plant genomes. Because their mobility can be potentially deleterious to the host, a variety of mechanisms evolved limiting that negative impact, one of them being preference for a specific target insertion site. Here, we describe a family of Mutator-like DNA transposons in Medicago truncatula targeting TA microsatellites. We identified 218 copies of MuTAnTs and an element carrying a complete ORF encoding a mudrA-like transposase. Most insertion sites are flanked by a variable number of TA tandem repeats, indicating that MuTAnTs are specifically targeting TA microsatellites. Other TE families flanked by TA repeats (e.g. TAFT elements in maize) were described previously, however we identified the first putative autonomous element sharing that characteristics with a related group of short non-autonomous transposons.
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13
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Terol J, Ibañez V, Carbonell J, Alonso R, Estornell LH, Licciardello C, Gut IG, Dopazo J, Talon M. Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation. BMC Genomics 2015; 16:69. [PMID: 25758634 PMCID: PMC4334395 DOI: 10.1186/s12864-015-1280-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 01/26/2015] [Indexed: 02/07/2023] Open
Abstract
Background Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored. Results Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5′ end of the deletion. The Arrufatina Mule displayed “dissimilar” 9-bp target site duplications separated by 2 Mb. Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome. Conclusions Taken together, this information is compatible with the proposal that in both mutants, the TTC-repeat motif formed a triplex DNA structure generating a loop that brought in close proximity the originally distinct reactive ends. In Arrufatina, the loop brought the Mule ends nearby the 2 distinct insertion target sites and the inverted insertion of the transposable element between these target sites provoked the release of the in-between fragment. This proposal requires the involvement of a unique transposon and sheds light on the unresolved question of how two distinct sites become located in close proximity. These observations confer a crucial role to the TTC-repeats in fundamental plant processes as meiotic recombination and chromosomal rearrangements. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1280-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - Victoria Ibañez
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - José Carbonell
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Roberto Alonso
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Leandro H Estornell
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - Concetta Licciardello
- CRA-ACM, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Corso Savoia 190, 95024, Acireale, Catania, Italy.
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028, Barcelona, Spain.
| | - Joaquín Dopazo
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
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14
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Zhao D, Ferguson A, Jiang N. Transposition of a rice Mutator-like element in the yeast Saccharomyces cerevisiae. THE PLANT CELL 2015; 27:132-148. [PMID: 25587002 PMCID: PMC4330571 DOI: 10.1105/tpc.114.128488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/30/2014] [Accepted: 12/24/2014] [Indexed: 06/04/2023]
Abstract
Mutator-like transposable elements (MULEs) are widespread in plants and are well known for their high transposition activity as well as their ability to duplicate and amplify host gene fragments. Despite their abundance and importance, few active MULEs have been identified. In this study, we demonstrated that a rice (Oryza sativa) MULE, Os3378, is capable of excising and reinserting in yeast (Saccharomyces cerevisiae), suggesting that yeast harbors all the host factors for the transposition of MULEs. The transposition activity induced by the wild-type transposase is low but can be altered by modification of the transposase sequence, including deletion, fusion, and substitution. Particularly, fusion of a fluorescent protein to the transposase enhanced the transposition activity, representing another approach to manipulate transposases. Moreover, we identified a critical region in the transposase where the net charge of the amino acids seems to be important for activity. Finally, transposition efficiency is also influenced by the element and its flanking sequences (i.e., small elements are more competent than their large counterparts). Perfect target site duplication is favorable, but not required, for precise excision. In addition to the potential application in functional genomics, this study provides the foundation for further studies of the transposition mechanism of MULEs.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Ann Ferguson
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
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15
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Zhao D, Jiang N. Nested insertions and accumulation of indels are negatively correlated with abundance of mutator-like transposable elements in maize and rice. PLoS One 2014; 9:e87069. [PMID: 24475224 PMCID: PMC3903597 DOI: 10.1371/journal.pone.0087069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/23/2013] [Indexed: 11/29/2022] Open
Abstract
Mutator-like transposable elements (MULEs) are widespread in plants and were first discovered in maize where there are a total of 12,900 MULEs. In comparison, rice, with a much smaller genome, harbors over 30,000 MULEs. Since maize and rice are close relatives, the differential amplification of MULEs raised an inquiry into the underlying mechanism. We hypothesize this is partly attributed to the differential copy number of autonomous MULEs with the potential to generate the transposase that is required for transposition. To this end, we mined the two genomes and detected 530 and 476 MULEs containing transposase sequences (candidate coding-MULEs) in maize and rice, respectively. Over 1/3 of the candidate coding-MULEs harbor nested insertions and the ratios are similar in the two genomes. Among the maize elements with nested insertions, 24% have insertions in coding regions and over half of them harbor two or more insertions. In contrast, only 12% of the rice elements have insertions in coding regions and 19% have multiple insertions, suggesting that nested insertions in maize are more disruptive. This is because most nested insertions in maize are from LTR retrotransposons, which are large in size and are prevalent in the maize genome. Our results suggest that the amplification of retrotransposons may limit the amplification of DNA transposons but not vice versa. In addition, more indels are detected among maize elements than rice elements whereas defects caused by point mutations are comparable between the two species. Taken together, more disruptive nested insertions combined with higher frequency of indels resulted in few (6%) coding-MULEs that may encode functional transposases in maize. In contrast, 35% of the coding-MULEs in rice retain putative intact transposase. This is in addition to the higher expression frequency of rice coding-MULEs, which may explain the higher occurrence of MULEs in rice than that in maize.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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16
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Li Y, Harris L, Dooner HK. TED, an autonomous and rare maize transposon of the mutator superfamily with a high gametophytic excision frequency. THE PLANT CELL 2013; 25:3251-65. [PMID: 24038653 PMCID: PMC3809530 DOI: 10.1105/tpc.113.116517] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor.
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Affiliation(s)
- Yubin Li
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854
| | - Linda Harris
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada K1A 0C6
| | - Hugo K. Dooner
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901
- Address correspondence to
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17
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Identification of an active Mutator-like element (MULE) in rice (Oryza sativa). Mol Genet Genomics 2012; 287:261-71. [PMID: 22274888 DOI: 10.1007/s00438-012-0676-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 01/12/2012] [Indexed: 10/14/2022]
Abstract
Transposable elements (TEs) represent an important fraction of plant genomes and play a significant role in gene and genome evolution. Among all TE superfamilies discovered in plants, Mutator from maize (Zea mays) is the most active and mutagenic element. Mutator-like elements (MULEs) were identified in a wide range of plants. However, only few active MULEs have been reported, and the transposition mechanism of the elements is still poorly understood. In this study, an active MULE named Os3378 was discovered in rice (Oryza sativa) by a combination of computational and experimental approaches. The four newly identified Os3378 elements share more than 98% sequence identity between each other, and all of them encode transposases without any deletion derivatives, indicating their capability of autonomous transposition. Os3378 is present in the rice species with AA genome type but is absent in other non-AA genome species. A new insertion of Os3378 was identified in a rice somaclonal mutant Z418, and the element remained active in the descendants of the mutant for more than ten generations. Both germinal and somatic excision events of Os3378 were observed, and no footprint was detected after excision. Furthermore, the occurrence of somatic excision of Os3378 appeared to be associated with plant developmental stages and tissue types. Taken together, Os3378 is a unique active element in rice, which provides a valuable resource for further studying of transposition mechanism and evolution of MULEs.
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18
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Smith AM, Hansey CN, Kaeppler SM. TCUP: A Novel hAT Transposon Active in Maize Tissue Culture. FRONTIERS IN PLANT SCIENCE 2012; 3:6. [PMID: 22639634 PMCID: PMC3355664 DOI: 10.3389/fpls.2012.00006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 01/04/2012] [Indexed: 05/08/2023]
Abstract
Transposable elements (TEs) are capable of inducing heritable de novo genetic variation. The sequences capable of reactivation, and environmental factors that induce mobilization, remain poorly defined even in well-studied genomes such as maize. We treated maize tissue culture with the demethylating agent 5-aza-2-deoxcytidine and examined long-term tissue culture lines to discover silenced TEs that have the potential to induce heritable genetic variation. Through these screens we have identified a novel low copy number hAT transposon, Tissue Culture Up-Regulated (TCUP), which is transcribed at high levels in long-term maize black Mexican sweet (BMS) tissue culture and is transcribed in response to treatment with 5-aza-2-deoxycytidine. Analysis of the TIGR Maize Gene Index revealed that this element is the most frequently represented EST from the BMS cell culture library and is not represented in other tissue libraries, which is the basis for its name. A full-length sequence was assembled in inbred B73 that contains the putative functional motifs required for autonomous movement of a hAT transposon. Transposon display detected novel TCUP insertions in two long-term tissue-cultured cell lines of the genotype Hi-II A × B and BMS. This research implicates TCUP as a transposon that is capable of reactivation and which may also be particularly sensitive to the stress of the tissue culture environment. Our findings are consistent with the hypothesis that epigenetic alterations potentiate genomic responses to stress during clonal propagation of plants.
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Affiliation(s)
| | - Candice N. Hansey
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Shawn M. Kaeppler
- Department of Agronomy, University of WisconsinMadison, WI, USA
- *Correspondence: Shawn M. Kaeppler, Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA. e-mail:
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19
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Gross SM, Williamson VM. Tm1: a mutator/foldback transposable element family in root-knot nematodes. PLoS One 2011; 6:e24534. [PMID: 21931741 PMCID: PMC3169594 DOI: 10.1371/journal.pone.0024534] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/11/2011] [Indexed: 11/18/2022] Open
Abstract
Three closely related parthenogenetic species of root-knot nematodes, collectively termed the Meloidogyne incognita-group, are economically significant pathogens of diverse crop species. Remarkably, these asexual root-knot nematodes are capable of acquiring heritable changes in virulence even though they lack sexual reproduction and meiotic recombination. Characterization of a near isogenic pair of M. javanica strains differing in response to tomato with the nematode resistance gene Mi-1 showed that the virulent strain carried a deletion spanning a gene called Cg-1. Herein, we present evidence that the Cg-1 gene lies within a member of a novel transposable element family (Tm1; Transposon in Meloidogyne-1). This element family is defined by composite terminal inverted repeats of variable lengths similar to those of Foldback (FB) transposable elements and by 9 bp target site duplications. In M. incognita, Tm1 elements can be classified into three general groups: 1) histone-hairpin motif elements; 2) MITE-like elements; 3) elements encoding a putative transposase. The predicted transposase shows highest similarity to gene products encoded by aphids and mosquitoes and resembles those of the Phantom subclass of the Mutator transposon superfamily. Interestingly, the meiotic, sexually-reproducing root-knot nematode species M. hapla has Tm1 elements with similar inverted repeat termini, but lacks elements with histone hairpin motifs and contains no elements encoding an intact transposase. These Tm1 elements may have impacts on root-knot nematode genomes and contribute to genetic diversity of the asexual species.
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Affiliation(s)
- Stephen M. Gross
- Department of Nematology, University of California Davis, Davis, California, United States of America
| | - Valerie M. Williamson
- Department of Nematology, University of California Davis, Davis, California, United States of America
- * E-mail:
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20
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Identification of an active new mutator transposable element in maize. G3-GENES GENOMES GENETICS 2011; 1:293-302. [PMID: 22384340 PMCID: PMC3276141 DOI: 10.1534/g3.111.000398] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 08/02/2011] [Indexed: 11/25/2022]
Abstract
Robertson’s Mutator (Mu) system has been used in large scale mutagenesis in maize, exploiting its high mutation frequency, controllability, preferential insertion in genes, and independence of donor location. Eight Mutator elements have been fully characterized (Mu1, Mu2 /Mu1.7, Mu3, Mu4, Mu5, Mu6/7, Mu8, MuDR), and three are defined by TIR (Mu10, Mu11 and Mu12). The genome sequencing revealed a complex family of Mu-like-elements (MULEs) in the B73 genome. In this article, we report the identification of a new Mu element, named Mu13. Mu13 showed typical Mu characteristics by having a ∼220 bp TIR, creating a 9 bp target site duplication upon insertion, yet the internal sequence is completely different from previously identified Mu elements. Mu13 is not present in the B73 genome or a Zea mays subsp. parviglumis accession, but in W22 and several inbreds that found the Robertson’s Mutator line. Analysis of mutants isolated from the UniformMu mutagenic population indicated that the Mu13 element is active in transposition. Two novel insertions were found in expressed genes. To test other unknown Mu elements, we selected six new Mu elements from the B73 genome. Southern analysis indicated that most of these elements were present in the UniformMu lines. From these results, we conclude that Mu13 is a new and active Mu element that significantly contributed to the mutagenesis in the UniformMu population. The Robertson’s Mutator line may harbor other unknown active Mu elements.
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21
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Curupira-1 and Curupira-2, two novel Mutator-like DNA transposons from the genomes of human parasites Schistosoma mansoni and Schistosoma japonicum. Parasitology 2011; 138:1124-33. [PMID: 21756422 DOI: 10.1017/s0031182011000886] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Transposons of the Mutator superfamily have been widely described in plants, but only recently have metazoan organisms been shown to harbour them. In this work we describe novel Mutator superfamily transposons from the genomes of the human parasites Schistosoma mansoni and S. japonicum, which we name Curupira-1 and Curupira-2. Curupira elements do not have Terminal Inverted Repeats (TIRs) at their extremities and generate Target Site Duplications (TSDs) of 9 base pairs. Curupira-2 transposons code for a conserved transposase and SWIM zinc finger domains, while Curupira-1 elements comprise these same domains plus a WRKY zinc finger. Alignment of transcript sequences from both elements back to the genomes indicates that they are subject to splicing to produce mature transcripts. Phylogenetic analyses indicate that these transposons represent a new lineage of metazoan Mutator-like elements with characteristics that are distinct from the recently described Phantom elements. Description of these novel schistosome transposons provides new insights in the evolution of transposable elements in schistosomes.
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Ouyang X, Li J, Li G, Li B, Chen B, Shen H, Huang X, Mo X, Wan X, Lin R, Li S, Wang H, Deng XW. Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. THE PLANT CELL 2011; 23:2514-35. [PMID: 21803941 PMCID: PMC3226222 DOI: 10.1105/tpc.111.085126] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 07/10/2011] [Accepted: 07/17/2011] [Indexed: 05/18/2023]
Abstract
FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), two transposase-derived transcription factors, are key components in phytochrome A signaling and the circadian clock. Here, we use chromatin immunoprecipitation-based sequencing (ChIP-seq) to identify 1559 and 1009 FHY3 direct target genes in darkness (D) and far-red (FR) light conditions, respectively, in the Arabidopsis thaliana genome. FHY3 preferentially binds to promoters through the FHY3/FAR1 binding motif (CACGCGC). Interestingly, FHY3 also binds to two motifs in the 178-bp Arabidopsis centromeric repeats. Comparison between the ChIP-seq and microarray data indicates that FHY3 quickly regulates the expression of 197 and 86 genes in D and FR, respectively. FHY3 also coregulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE5 and ELONGATED HYPOCOTYL5. Moreover, we uncover a role for FHY3 in controlling chloroplast development by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5, whose product is a structural component of the latter stages of chloroplast division in Arabidopsis. Taken together, our data suggest that FHY3 regulates multiple facets of plant development, thus providing insights into its functions beyond light and circadian pathways.
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Affiliation(s)
- Xinhao Ouyang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Rice Research Institute of Sichuan Agriculture University, Chengdu, Sichuan 611130, China
| | - Jigang Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
| | - Gang Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Bosheng Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Beibei Chen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Huaishun Shen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xi Huang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xiaorong Mo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xiangyuan Wan
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shigui Li
- Rice Research Institute of Sichuan Agriculture University, Chengdu, Sichuan 611130, China
| | - Haiyang Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
| | - Xing Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
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23
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Meng Q, Chen K, Ma L, Hu S, Yu J. A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases. J Genet Genomics 2011; 38:63-70. [PMID: 21356525 DOI: 10.1016/j.jcg.2011.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 02/03/2023]
Abstract
Transposons are sequence elements widely distributed among genomes of all three kingdoms of life, providing genomic changes and playing significant roles in genome evolution. Trichomonas vaginalis is an excellent model system for transposon study since its genome (~160 Mb) has been sequenced and is composed of ~65% transposons and other repetitive elements. In this study, we primarily report the identification of Kolobok-type transposons (termed tvBac) in T. vaginalis and the results of transposase sequence analysis. We categorized 24 novel subfamilies of the Kolobok element, including one autonomous subfamily and 23 non-autonomous subfamilies. We also identified a novel H2CH motif in tvBac transposases based on multiple sequence alignment. In addition, we supposed that tvBac and Mutator transposons may have evolved independently from a common ancestor according to our phylogenetic analysis. Our results provide basic information for the understanding of the function and evolution of tvBac transposons in particular and other related transposon families in general.
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Affiliation(s)
- Qingshu Meng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
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24
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Marquez CP, Pritham EJ. Phantom, a new subclass of Mutator DNA transposons found in insect viruses and widely distributed in animals. Genetics 2010; 185:1507-17. [PMID: 20457878 PMCID: PMC2927773 DOI: 10.1534/genetics.110.116673] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposons of the Mutator (Mu) superfamily have been shown to play a critical role in the evolution of plant genomes. However, the identification of Mutator transposons in other eukaryotes has been quite limited. Here we describe a previously uncharacterized group of DNA transposons designated Phantom identified in the genomes of a wide range of eukaryotic taxa, including many animals, and provide evidence for its inclusion within the Mutator superfamily. Interestingly three Phantom proteins were also identified in two insect viruses and phylogenetic analysis suggests horizontal movement from insect to virus, providing a new line of evidence for the role of viruses in the horizontal transfer of DNA transposons in animals. Many of the Phantom transposases are predicted to harbor a FLYWCH domain in the amino terminus, which displays a WRKY-GCM1 fold characteristic of the DNA binding domain (DBD) of Mutator transposases and of several transcription factors. While some Phantom elements have terminal inverted repeats similar in length and structure to Mutator elements, some display subterminal inverted repeats (sub-TIRs) and others have more complex termini reminiscent of so-called Foldback (FB) transposons. The structural plasticity of Phantom and the distant relationship of its encoded protein to known transposases may have impeded the discovery of this group of transposons and it suggests that structure in itself is not a reliable character for transposon classification.
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Affiliation(s)
- Claudia P Marquez
- Department of Biology, University of Texas, Arlington, Texas 76019, USA
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25
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Shan XH, Ou XF, Liu ZL, Dong YZ, Lin XY, Li XW, Liu B. Transpositional activation of mPing in an asymmetric nuclear somatic cell hybrid of rice and Zizania latifolia was accompanied by massive element loss. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1325-33. [PMID: 19711051 DOI: 10.1007/s00122-009-1137-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Accepted: 08/12/2009] [Indexed: 05/09/2023]
Abstract
We have reported previously that the most active miniature inverted terminal repeat transposable element (MITE) of rice, mPing, was transpositionally mobilized in several rice recombinant inbred lines (RILs) derived from an introgressive hybridization between rice and wild rice (Zizania latifolia Griseb.). To further study the phenomenon of hybridization-induced mPing activity, we undertook the present study to investigate the element's behavior in a highly asymmetric somatic nuclear hybrid (SH6) of rice and Z. latifolia, which is similar in genomic composition to that of the RILs, though probably contains more introgressed alien chromatins from the donor species than the RILs. We found that mPing, together with its transposase-donor, Pong, underwent rampant transpositional activation in the somatic hybrid (SH6). Because possible effects of protoplast isolation and cell culture can be ruled out, we attribute the transpositional activation of mPing and Pong in SH6 to the process of asymmetric somatic hybridization, namely, one-step introgression of multiple chromatin segments of the donor species Z. latifolia into the recipient rice genome. A salient feature of mPing transposition in the somatic hybrid is that the element's activation was accompanied by massive loss of its original copies, i.e., abortive transpositions, which was not observed in previously reported cases of mPing activity. These data not only corroborated our earlier finding that wide hybridization and introgression may trigger transpositional activation of otherwise quiescent transposable elements, but also suggest that transpositional mobilization of a MITE like mPing can be accompanied by dramatic reduction of its original copy numbers under certain conditions, thus provide novel insights into the dynamics of MITEs in the course of genome evolution.
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Affiliation(s)
- X H Shan
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, 130024 Changchun, China
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Abstract
Mutator (Mu) is by far the most mutagenic plant transposon. The high frequency of transposition and the tendency to insert into low copy sequences for such transposon have made it the primary means by which genes are mutagenized in maize (Zea mays L.). Mus like elements (MULEs) are widespread among angiosperms and multiple-diverged functional variants can be present in a single genome. MULEs often capture genetic sequences. These Pack-MuLEs can mobilize thousands of gene fragments, which may have had a significant impact on host genome evolution. There is also evidence that MULEs can move between reproductively isolated species. Here we present an overview of the discovery, features and utility of Mu transposon. Classification of Mu elements and future directions of related research are also discussed. Understanding Mu will help us elucidate the dynamic genome.
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Affiliation(s)
- Xian-Min Diao
- National Millet Improvement Center of China, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang.
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27
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Hua-Van A, Capy P. Analysis of the DDE motif in the Mutator superfamily. J Mol Evol 2009; 67:670-81. [PMID: 19018586 DOI: 10.1007/s00239-008-9178-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 10/16/2008] [Indexed: 01/29/2023]
Abstract
The eukaryotic Mutator family of transposable elements is widespread in plants. Active or potentially active copies are also found in fungi and protozoans, and sequences related to this family have been detected in metazoans as well. Members of this family are called Mutator-like elements (MULEs). They encode transposases, which contain a region conserved with transposases of the IS256 prokaryotic family, known to harbor a DDE catalytic domain. Different DDE or D34E motifs have been proposed in some groups of eukaryotic MULEs based on primary sequence conservation. On a large number of protein sequences related to, and representative of, all MULE families, we analyzed global conservation, the close environment of different acidic residues and the secondary structure. This allowed us to identify a potential DDE motif that is likely to be homologous to the one in IS256-like transposases. The characteristics of this motif are depicted in each known family of MULEs. Different hypotheses about the evolution of this triad are discussed.
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Affiliation(s)
- Aurélie Hua-Van
- Laboratoire Evolution, Génomes et Spéciation UPR9034, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France.
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28
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Hanada K, Vallejo V, Nobuta K, Slotkin RK, Lisch D, Meyers BC, Shiu SH, Jiang N. The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. THE PLANT CELL 2009; 21:25-38. [PMID: 19136648 PMCID: PMC2648092 DOI: 10.1105/tpc.108.063206] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Gene duplication is an important mechanism for evolution of new genes. In plants, a special group of transposable elements, called Pack-MULEs or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. Despite the abundance of Pack-MULEs, the functionality of these duplicates is not clear. Here, we present a comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes. At least 22% of the Pack-MULEs are transcribed, and 28 Pack-MULEs have direct evidence of translation. Chimeric Pack-MULEs, which contain gene fragments from multiple genes, are much more frequently expressed than those derived only from a single gene. In addition, Pack-MULEs are frequently associated with small RNAs. The presence of these small RNAs is associated with a reduction in expression of both the Pack-MULEs and their parental genes. Furthermore, an assessment of the selection pressure on the Pack-MULEs using the ratio of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number of Pack-MULEs likely have been under selective constraint. The Ka/Ks values of Pack-MULE and parental gene pairs are lower among Pack-MULEs that are expressed in sense orientations. Taken together, our analysis suggests that a significant number of Pack-MULEs are expressed and subjected to purifying selection, and some are associated with small RNAs. Therefore, at least a subset of Pack-MULEs are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.
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Affiliation(s)
- Kousuke Hanada
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
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29
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Lin R, Teng Y, Park HJ, Ding L, Black C, Fang P, Wang H. Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction. PLANT PHYSIOLOGY 2008; 148:981-92. [PMID: 18715961 PMCID: PMC2556831 DOI: 10.1104/pp.108.120436] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 08/15/2008] [Indexed: 05/20/2023]
Abstract
Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. We recently showed that Arabidopsis (Arabidopsis thaliana) FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), a pair of homologous proteins sharing significant sequence homology to Mutator-like transposases, act as novel transcription factors essential for activating the expression of FHY1 and FHL (for FHY1-like), whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses. FHY3, FAR1, and Mutator-like transposases also share a similar domain structure, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). In this study, we performed a promoter-swapping analysis of FHY3 and FAR1. Our results suggest that the partially overlapping functions of FHY3 and FAR1 entail divergence of their promoter activities and protein subfunctionalization. To gain a better understanding of the molecular mode of FHY3 function, we performed a structure-function analysis, using site-directed mutagenesis and transgenic approaches. We show that the conserved N-terminal C2H2 zinc finger domain is essential for direct DNA binding and biological function of FHY3 in mediating light signaling, whereas the central core transposase domain and C-terminal SWIM domain are essential for the transcriptional regulatory activity of FHY3 and its homodimerization or heterodimerization with FAR1. Furthermore, the ability to form homodimers or heterodimers largely correlates with the transcriptional regulatory activity of FHY3 in plant cells. Together, our results reveal discrete roles of the multiple domains of FHY3 and provide functional support for the proposition that FHY3 and FAR1 represent transcription factors derived from a Mutator-like transposase(s).
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Affiliation(s)
- Rongcheng Lin
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
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30
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Scholthof KBG, Jackson AO, Van Etten JL. Myron Kendall Brakke: 1921 to 2007. PHYTOPATHOLOGY 2008; 98:1056-1059. [PMID: 18943450 DOI: 10.1094/phyto-98-10-1056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Karen-Beth G Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station 77843-2132, USA.
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31
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Benjak A, Forneck A, Casacuberta JM. Genome-wide analysis of the "cut-and-paste" transposons of grapevine. PLoS One 2008; 3:e3107. [PMID: 18769592 PMCID: PMC2528002 DOI: 10.1371/journal.pone.0003107] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 08/10/2008] [Indexed: 01/30/2023] Open
Abstract
Background The grapevine is a widely cultivated crop and a high number of different varieties have been selected since its domestication in the Neolithic period. Although sexual crossing has been a major driver of grapevine evolution, its vegetative propagation enhanced the impact of somatic mutations and has been important for grapevine diversity. Transposable elements are known to be major contributors to genome variability and, in particular, to somatic mutations. Thus, transposable elements have probably played a major role in grapevine domestication and evolution. The recent publication of the complete grapevine genome opens the possibility for an in deep analysis of its transposon content. Principal Findings We present here a detailed analysis of the “cut-and-paste” class II transposons present in the genome of grapevine. We characterized 1160 potentially complete grapevine transposons as well as 2086 defective copies. We report on the structure of each element, their potentiality to encode a functional transposase, and the existence of matching ESTs that could suggest their transcription. Conclusions Our results show that these elements have transduplicated and amplified cellular sequences and some of them have been domesticated and probably fulfill cellular functions. In addition, we provide evidences that the mobility of these elements has contributed to the genomic variability of this species.
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Affiliation(s)
- Andrej Benjak
- Departament de Genètica Molecular Vegetal, Centre de Recerca en Agrigenòmica (CRAG), Barcelona, Spain
- Institute of Horticulture and Viticulture, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Astrid Forneck
- Institute of Horticulture and Viticulture, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Josep M. Casacuberta
- Departament de Genètica Molecular Vegetal, Centre de Recerca en Agrigenòmica (CRAG), Barcelona, Spain
- * E-mail:
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32
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Bouvet GF, Jacobi V, Plourde KV, Bernier L. Stress-induced mobility of OPHIO1 and OPHIO2, DNA transposons of the Dutch elm disease fungi. Fungal Genet Biol 2008; 45:565-78. [DOI: 10.1016/j.fgb.2007.12.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 12/09/2007] [Accepted: 12/10/2007] [Indexed: 01/27/2023]
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33
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Asakura N, Yoshida S, Mori N, Ohtsuka I, Nakamura C. Sequence diversity and copy number variation of Mutator-like transposases in wheat. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000300022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | - Shinya Yoshida
- Hyogo Institute of Agriculture, Forestry & Fisheries, Japan
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34
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Dooner HK, Weil CF. Give-and-take: interactions between DNA transposons and their host plant genomes. Curr Opin Genet Dev 2007; 17:486-92. [PMID: 17919898 DOI: 10.1016/j.gde.2007.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Revised: 07/31/2007] [Accepted: 08/27/2007] [Indexed: 12/18/2022]
Abstract
Recent genome sequencing efforts have revealed how extensively transposable elements (TEs) have contributed to the shaping of present day plant genomes. DNA transposons associate preferentially with the euchromatic or genic component of plant genomes and have had the opportunity to interact intimately with the genes of the plant host. These interactions have resulted in TEs acquiring host sequences, forming chimeric genes through exon shuffling, replacing regulatory sequences, mobilizing genes around the genome, and contributing genes to the host. The close interaction of transposons with genes has also led to the evolution of intricate cellular mechanisms for silencing transposon activity. Transposons have thus become important subjects of study in understanding epigenetic regulation and, in cases where transposons have amplified to high numbers, how to escape that regulation.
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Affiliation(s)
- Hugo K Dooner
- Waksman Institute, Rutgers University, Piscataway, NJ 08854-8020, USA.
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35
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Sun G, Daley T, Ni Y. Molecular evolution and genome divergence at RPB2 gene of the St and H genome in Elymus species. PLANT MOLECULAR BIOLOGY 2007; 64:645-55. [PMID: 17551673 DOI: 10.1007/s11103-007-9183-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Accepted: 05/04/2007] [Indexed: 05/15/2023]
Abstract
Molecular evolution of the second largest subunit of low copy nuclear RNA polymerase II (RPB2) in allotetrploid StH genomic species of Elymus is characterized here. Our study first reported a 39-bp MITE stowaway element insertion in the genic region of RPB2 gene for all tetraploid Elymus St genome and diploid Pseudoroegneria spicata and P. stipifolia St genome. The sequences on 3'-end are highly conserved, with AGTA in all sequences but H10339 (E. fibrosis), in which the AGTA was replaced with AGAA. All 12 Stowaway-containing sequences encompassed a 9 bp conserved TIRs (GAGGGAGTA). Interestingly, the 5'-end sequence of GGTA which was changed to AGTA or deleted resulted in Stowaway excision in the H genome of Elymus sepcies, in which Stowaway excision did not leave footprint. Another two large insertions in all St genome sequences are also transposable-like elements detected in the genic region of RPB2 gene. Our results indicated that these three transposable element indels have occurred prior to polyploidization, and shaped the homoeologous RPB2 loci in St and H genome of Eymus species. Nucleotide diversity analysis suggested that the RPB2 sequence may evolve faster in the polyploid species than in the diploids. Higher level of polymorphism and genome-specific amplicons generated by this gene indicated that RPB2 is an excellent tool for investigating the phylogeny and evolutionary dynamics of speciation, and the mode of polyploidy formation in Elymus species.
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Affiliation(s)
- Genlou Sun
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS, Canada, B3H 3C3.
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36
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Yang G, Zhang F, Hancock CN, Wessler SR. Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2007; 104:10962-7. [PMID: 17578919 PMCID: PMC1904124 DOI: 10.1073/pnas.0702080104] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An active miniature inverted repeat transposable element (MITE), mPing, was discovered by computer-assisted analysis of rice genome sequence. The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1,000 copies during recent domestication. However, determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome. Here, we report that mPing is active in Arabidopsis thaliana, where its transposition is catalyzed by three sources of transposase from rice: the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript. In addition to transposase, the product of a second element-encoded ORF of unknown function is also required for mPing transposition. Excision of mPing in A. thaliana is usually precise, and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes. As such, this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes.
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Affiliation(s)
- Guojun Yang
- Department of Plant Biology, University of Georgia, Athens, GA 30602
| | - Feng Zhang
- Department of Plant Biology, University of Georgia, Athens, GA 30602
| | - C. Nathan Hancock
- Department of Plant Biology, University of Georgia, Athens, GA 30602
| | - Susan R. Wessler
- Department of Plant Biology, University of Georgia, Athens, GA 30602
- *To whom correspondence should be addressed at:
4505 Miller Plant Sciences Building, University of Georgia, Athens, GA 30602. E-mail:
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37
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Barret P, Brinkman M, Beckert M. A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize. Genome 2007; 49:1399-407. [PMID: 17426755 DOI: 10.1139/g06-109] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are nonautonomous elements that are abundant in plant genomes. The rice MITE mPing was shown to be mobilized by anther culture, and the associated transposon Pong was shown to transpose actively in an Oryza sativa 'indica' rice cell-culture line. We have identified 3 sequences in maize named ZmTPAPong-like 1, 2, and 3 that displayed homology with the transposase of Pong. Here, we show that these sequences are differentially expressed during the in vitro androgenetic process in maize. We also demonstrate that the ZmTPAPong-like 1 and 3 sequences reveal somaclonal variations among plants regenerated from the calli of a doubled haploid line. These data suggest that the ZmTPAPong-like sequences could form part of a Zea mays element related to the rice Pong element. The possible activation of this newly discovered element under stress conditions is discussed.
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Affiliation(s)
- P Barret
- INRA, UMR INRA-UBP Amélioration et Santé des Plantes, 63,000 Clermont-Ferrand, France.
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Holligan D, Zhang X, Jiang N, Pritham EJ, Wessler SR. The transposable element landscape of the model legume Lotus japonicus. Genetics 2006; 174:2215-28. [PMID: 17028332 PMCID: PMC1698628 DOI: 10.1534/genetics.106.062752] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 09/18/2006] [Indexed: 11/18/2022] Open
Abstract
The largest component of plant and animal genomes characterized to date is transposable elements (TEs). The availability of a significant amount of Lotus japonicus genome sequence has permitted for the first time a comprehensive study of the TE landscape in a legume species. Here we report the results of a combined computer-assisted and experimental analysis of the TEs in the 32.4 Mb of finished TAC clones. While computer-assisted analysis facilitated a determination of TE abundance and diversity, the availability of complete TAC sequences permitted identification of full-length TEs, which facilitated the design of tools for genomewide experimental analysis. In addition to containing all TE types found in previously characterized plant genomes, the TE component of L. japonicus contained several surprises. First, it is the second species (after Oryza sativa) found to be rich in Pack-MULEs, with >1000 elements that have captured and amplified gene fragments. In addition, we have identified what appears to be a legume-specific MULE family that was previously identified only in fungal species. Finally, the L. japonicus genome contains many hundreds, perhaps thousands of Sireviruses: Ty1/copia-like elements with an extra ORF. Significantly, several of the L. japonicus Sireviruses have recently amplified and may still be actively transposing.
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Affiliation(s)
- Dawn Holligan
- Department of Plant Biology, University of Georgia, Athens 30602, USA
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39
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van Leeuwen H, Monfort A, Puigdomenech P. Mutator-like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains. Mol Genet Genomics 2006; 277:357-64. [PMID: 17136348 DOI: 10.1007/s00438-006-0194-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 11/05/2006] [Indexed: 01/22/2023]
Abstract
The transposon Mutator was first identified in maize, and is one of the most active mobile elements in plants. The Arabidopsis thaliana genome contains at least 200 Mutator-like elements (MULEs), which contain the Mutator-like transposase gene, and often additional genes. We have detected a novel type of MULEs in melon (CUMULE), which, besides the transposase, contains two ubiquitin-like specific protease-like sequences (ULP1). This element is not present in the observed location in some melon cultivars. Multiple copies of this element exist in the Cucumis melo genome, and it has been detected in other Cucurbitaceae species. Analysis of the A. thaliana genome revealed more than 90 CUMULE-like elements, containing one or two Ulp1-like sequences, although no evidence of mobility exists for these elements. We detected various putative transposable elements containing ULP1-like sequences in rice. The discovery of these MULEs in melon and Arabidopsis, and the existence of similar elements in rice and maize, suggest that a proteolytic function may be important for this subset of the MULE transposable elements.
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Affiliation(s)
- Hans van Leeuwen
- Departament de Genètica Molecular, Laboratori de Genètica Molecular Vegetal, CSIC-IRTA, Jordi Girona 18, 08034, Barcelona, Spain
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40
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Wang Q, Dooner HK. Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci U S A 2006; 103:17644-9. [PMID: 17101975 PMCID: PMC1693800 DOI: 10.1073/pnas.0603080103] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maize is probably the most diverse of all crop species. Unexpectedly large differences among haplotypes were first revealed in a comparison of the bz genomic regions of two different inbred lines, McC and B73. Retrotransposon clusters, which comprise most of the repetitive DNA in maize, varied markedly in makeup, and location relative to the genes in the region and genic sequences, later shown to be carried by two helitron transposons, also differed between the inbreds. Thus, the allelic bz regions of these Corn Belt inbreds shared only a minority of the total sequence. To investigate further the variation caused by retrotransposons, helitrons, and other insertions, we have analyzed the organization of the bz genomic region in five additional cultivars selected because of their geographic and genetic diversity: the inbreds A188, CML258, and I137TN, and the land races Coroico and NalTel. This vertical comparison has revealed the existence of several new helitrons, new retrotransposons, members of every superfamily of DNA transposons, numerous miniature elements, and novel insertions flanked at either end by TA repeats, which we call TAFTs (TA-flanked transposons). The extent of variation in the region is remarkable. In pairwise comparisons of eight bz haplotypes, the percentage of shared sequences ranges from 25% to 84%. Chimeric haplotypes were identified that combine retrotransposon clusters found in different haplotypes. We propose that recombination in the common gene space greatly amplifies the variability produced by the retrotransposition explosion in the maize ancestry, creating the heterogeneity in genome organization found in modern maize.
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Affiliation(s)
- Qinghua Wang
- *The Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08855; and
| | - Hugo K. Dooner
- *The Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08855; and
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901
- To whom correspondence should be addressed. E-mail:
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Ohtsu K, Hirano HY, Tsutsumi N, Hirai A, Nakazono M. Anaconda, a new class of transposon belonging to the Mu superfamily, has diversified by acquiring host genes during rice evolution. Mol Genet Genomics 2005; 274:606-15. [PMID: 16208489 DOI: 10.1007/s00438-005-0053-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
A new type of transposon, named Anaconda (Anac) has been found in rice (Oryza sativa). In this paper, we demonstrate that Anaconda elements have diversified by acquisition of host cellular genes, amplification of the elements, and substitution and deletion of short segments. We identified four Anaconda elements in studies of rice alternative oxidase (AOX) genes, and subsequently isolated an additional 23 elements based on the identity of their terminal inverted repeats (TIRs). The Anaconda elements have long TIRs (114-458 bp). They also have direct repeats of 9 or 10 bp in their flanking regions that are thought to have been generated upon transposition. These structural features reveal that the Anaconda elements belong to the Mu superfamily. The most prominent feature of the Anaconda elements is the high frequency with which they have acquired host cellular genes. Of the 27 elements found here, 19 appear to have sequences presumably derived from rice genes, for example, the genes for AOX1c (four elements), cytochrome P450 (five elements), L: -asparaginase (five elements), and PCF8 (two elements). Four elements, AnacA1-A4, have both the AOX1c and P450 genes. One element, AnacB14, involves a gene similar to mudrA of maize MuDR. Database analyses revealed that the loci of 26 of the 27 Anaconda elements in the subspecies japonica are the same as those in the subspecies indica. This suggests that these elements were incorporated before the divergence of these two subspecies.
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Affiliation(s)
- Kazuhiro Ohtsu
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, 113-8657, Tokyo, Japan.
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42
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Pritham EJ, Feschotte C, Wessler SR. Unexpected Diversity and Differential Success of DNA Transposons in Four Species of Entamoeba Protozoans. Mol Biol Evol 2005; 22:1751-63. [PMID: 15901838 DOI: 10.1093/molbev/msi169] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report the first comprehensive analysis of transposable element content in the compact genomes (approximately 20 Mb) of four species of Entamoeba unicellular protozoans for which draft sequences are now available. Entamoeba histolytica and Entamoeba dispar, two human parasites, have many retrotransposons, but few DNA transposons. In contrast, the reptile parasite Entamoeba invadens and the free-living Entamoeba moshkovskii contain few long interspersed elements but harbor diverse and recently amplified populations of DNA transposons. Representatives of three DNA transposase superfamilies (hobo/Activator/Tam3, Mutator, and piggyBac) were identified for the first time in a protozoan species in addition to a variety of members of a fourth superfamily (Tc1/mariner), previously reported only from ciliates and Trichomonas vaginalis among protozoans. The diversity of DNA transposons and their differential amplification among closely related species with similar compact genomes are discussed in the context of the biology of Entamoeba protozoans.
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Affiliation(s)
- Ellen J Pritham
- Department of Plant Biology, The University of Georgia, USA.
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Xu Z, Dooner HK. Mx-rMx, a family of interacting transposons in the growing hAT superfamily of maize. THE PLANT CELL 2005; 17:375-88. [PMID: 15659635 PMCID: PMC548813 DOI: 10.1105/tpc.104.027797] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Accepted: 11/16/2004] [Indexed: 05/19/2023]
Abstract
More than half a century after the discovery of transposable elements, the number of genetically defined autonomous elements that have been isolated and characterized molecularly in any one species remains surprisingly small. Because of its rich genetic history, maize (Zea mays) is, by far, the plant with the largest number of such elements. Yet, even in maize, a maximum of only two autonomous elements have been characterized in any transposon superfamily. This article describes the isolation and molecular and genetic characterization of Mx (for mobile element induced by x-rays), a third autonomous member of the hAT transposon superfamily in maize. Mx is 3731 bp long, ends in 13-bp terminal inverted repeats (TIRs), and causes an 8-bp duplication of the target site. Mx and rMx (for responder to Mx), its 571-bp nonautonomous partner, define a classical family of interacting transposable elements. Surprisingly, the TIRs of Mx and rMx are only 73% identical, and the subterminal sequences are even less so, suggesting that Mx and rMx may represent diverging transposable elements still capable of mobilization by the same transposase. Sequences that are closer to the ends of either Mx or rMx are present in the maize genome. Mx is predicted to encode a 674-amino acid protein that is homologous to the Ac transposase. Although Mx and Ac are closely related, they do not interact. Other data suggest that maize may possess at least five families of hAT transposons that do not interact with each other. The possible origin of noninteracting transposon families within the same superfamily is discussed.
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Affiliation(s)
- Zhennan Xu
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08855, USA
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Shan X, Liu Z, Dong Z, Wang Y, Chen Y, Lin X, Long L, Han F, Dong Y, Liu B. Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.). Mol Biol Evol 2005; 22:976-90. [PMID: 15647520 DOI: 10.1093/molbev/msi082] [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] [Indexed: 12/16/2022] Open
Abstract
Hybridization between different species plays an important role in plant genome evolution, as well as is a widely used approach for crop improvement. McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated. However, direct experimental evidence showing a causal relationship between plant wide hybridization and transposon mobilization has not yet been reported. The miniature-Ping (mPing) is a recently isolated active miniature inverted-repeat transposable element transposon from rice, which is mobilized by tissue culture and gamma-ray irradiation. We show herein that mPing, together with its putative transposase-encoding partner, Pong, is mobilized in three homologous recombinant inbred lines (RILs), derived from hybridization between rice (cultivar Matsumae) and wild rice (Zizania latifolia Griseb.), harboring introgressed genomic DNA from wild rice. In contrast, both elements remain immobile in two lines sharing the same parentage to the RILs but possessing no introgressed DNA. Thus, we have presented direct evidence that is consistent with McClintock's insight by demonstrating a causal link between wide hybridization and transposon mobilization in rice. In addition, we report an atypical behavior of mPing/Pong mobilization in these lines, i.e., the exclusive absence of footprints after excision.
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Affiliation(s)
- Xiaohui Shan
- Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
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