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Zhang T, Tan S, Tang N, Li Y, Zhang C, Sun J, Guo Y, Gao H, Cai Y, Sun W, Wang C, Fu L, Ma H, Wu Y, Hu X, Zhang X, Gee P, Yan W, Zhao Y, Chen Q, Guo B, Wang H, Zhang YE. Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox. Cell 2024; 187:3741-3760.e30. [PMID: 38843831 DOI: 10.1016/j.cell.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/11/2024] [Accepted: 05/02/2024] [Indexed: 07/14/2024]
Abstract
Experimental studies on DNA transposable elements (TEs) have been limited in scale, leading to a lack of understanding of the factors influencing transposition activity, evolutionary dynamics, and application potential as genome engineering tools. We predicted 130 active DNA TEs from 102 metazoan genomes and evaluated their activity in human cells. We identified 40 active (integration-competent) TEs, surpassing the cumulative number (20) of TEs found previously. With this unified comparative data, we found that the Tc1/mariner superfamily exhibits elevated activity, potentially explaining their pervasive horizontal transfers. Further functional characterization of TEs revealed additional divergence in features such as insertion bias. Remarkably, in CAR-T therapy for hematological and solid tumors, Mariner2_AG (MAG), the most active DNA TE identified, largely outperformed two widely used vectors, the lentiviral vector and the TE-based vector SB100X. Overall, this study highlights the varied transposition features and evolutionary dynamics of DNA TEs and increases the TE toolbox diversity.
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Affiliation(s)
- Tongtong Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Tang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yuanqing Li
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenze Zhang
- National Key Laboratory of Efficacy and Mechanism on Chinese Medicine for Metabolic Diseases, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jing Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Guo
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Gao
- Rengene Biotechnology Co., Ltd., Beijing 100036, China
| | - Yujia Cai
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxin Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Liangzheng Fu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yachao Wu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxuan Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuechun Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Peter Gee
- MaxCyte Inc., Rockville, MD 20850, USA
| | - Weihua Yan
- Cold Spring Biotech Corp., Beijing 100031, China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Baocheng Guo
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Haoyi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:172-192. [PMID: 35959634 PMCID: PMC9804982 DOI: 10.1111/tpj.15938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a basal eudicot plant with a unique lifestyle, physiological features, and evolutionary characteristics. Here we report the unique profile of transposable elements (TEs) in the genome, using a manually curated repeat library. TEs account for 59% of the genome, and hAT (Ac/Ds) elements alone represent 8%, more than in any other known plant genome. About 18% of the lotus genome is comprised of Copia LTR retrotransposons, and over 25% of them are associated with non-canonical termini (non-TGCA). Such high abundance of non-canonical LTR retrotransposons has not been reported for any other organism. TEs are very abundant in genic regions, with retrotransposons enriched in introns and DNA transposons primarily in flanking regions of genes. The recent insertion of TEs in introns has led to significant intron size expansion, with a total of 200 Mb in the 28 455 genes. This is accompanied by declining TE activity in intergenic regions, suggesting distinct control efficacy of TE amplification in different genomic compartments. Despite the prevalence of TEs in genic regions, some genes are associated with fewer TEs, such as those involved in fruit ripening and stress responses. Other genes are enriched with TEs, and genes in epigenetic pathways are the most associated with TEs in introns, indicating a dynamic interaction between TEs and the host surveillance machinery. The dramatic differential abundance of TEs with genes involved in different biological processes as well as the variation of target preference of different TEs suggests the composition and activity of TEs influence the path of evolution.
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Affiliation(s)
- Stefan Cerbin
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Ecology & Evolutionary BiologyUniversity of Kansas1200 Sunnyside AvenueLawrenceKS66045USA
| | - Shujun Ou
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yang Li
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Yanni Sun
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Ning Jiang
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
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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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Sahebi M, Hanafi MM, van Wijnen AJ, Rice D, Rafii MY, Azizi P, Osman M, Taheri S, Bakar MFA, Isa MNM, Noor YM. Contribution of transposable elements in the plant's genome. Gene 2018; 665:155-166. [PMID: 29684486 DOI: 10.1016/j.gene.2018.04.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/04/2018] [Accepted: 04/18/2018] [Indexed: 12/26/2022]
Abstract
Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed M Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | | | - David Rice
- Department of Molecular Biology & Biotecnology, University of Sheffield, United Kingdom
| | - M Y Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamad Osman
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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Cerbin S, Jiang N. Duplication of host genes by transposable elements. Curr Opin Genet Dev 2018; 49:63-69. [PMID: 29571044 DOI: 10.1016/j.gde.2018.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/12/2022]
Abstract
The availability of large amounts of genomic and transcriptome sequences have allowed systematic surveys about the host gene sequences that have been duplicated by transposable elements. It is now clear that all super-families of transposons are capable of duplicating genes or gene fragments, and such incidents have been detected in a wide spectrum of organisms. Emerging evidence suggests that a considerable portion of them function as coding or non-coding sequences, driving innovations at molecular and phenotypic levels. Interestingly, the duplication events not only have to occur in the reproductive tissues to become heritable, but the duplicated copies are also preferentially expressed in those tissues. As a result, reproductive tissues may serve as the 'incubator' for genes generated by transposable elements.
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Affiliation(s)
- Stefan Cerbin
- Department of Horticulture, 1066 Bogue Street, Michigan State University, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, 1066 Bogue Street, Michigan State University, East Lansing, MI 48824, USA.
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Liu K, Wessler SR. Transposition of Mutator-like transposable elements (MULEs) resembles hAT and Transib elements and V(D)J recombination. Nucleic Acids Res 2017; 45:6644-6655. [PMID: 28482040 PMCID: PMC5499845 DOI: 10.1093/nar/gkx357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/13/2017] [Accepted: 04/20/2017] [Indexed: 12/11/2022] Open
Abstract
Mutator-like transposable elements (MULEs) are widespread across fungal, plant and animal species. Despite their abundance and importance as genetic tools in plants, the transposition mechanism of the MULE superfamily was previously unknown. Discovery of the Muta1 element from Aedes aegypti and its successful transposition in yeast facilitated the characterization of key steps in Muta1 transposition. Here we show that purified transposase binds specifically to the Muta1 ends and catalyzes excision through double strand breaks (DSB) and the joining of newly excised transposon ends with target DNA. In the process, the DSB forms hairpin intermediates on the flanking DNA side. Analysis of transposase proteins containing site-directed mutations revealed the importance of the conserved DDE motif and a W residue. The transposition pathway resembles that of the V(D)J recombination reaction and the mechanism of hAT and Transib transposases including the importance of the conserved W residue in both MULEs and hATs. In addition, yeast transposition and in vitro assays demonstrated that the terminal motif and subterminal repeats of the Muta1 terminal inverted repeat also influence Muta1 transposition. Collectively, our data provides new insights to understand the evolutionary relationships between MULE, hAT and Transib elements and the V(D)J recombinase.
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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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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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Kang H, Zhu D, Lin R, Opiyo SO, Jiang N, Shiu SH, Wang GL. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads. DNA Res 2016; 23:241-51. [PMID: 27098848 PMCID: PMC4909310 DOI: 10.1093/dnares/dsw011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/21/2016] [Indexed: 11/16/2022] Open
Abstract
Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. PTEMD and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm.
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Affiliation(s)
- Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dan Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China Department of Agronomy, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Runmao Lin
- Department of Plant Pathology, Institute of Vegetables and flowers, Chinese Academy of Agriculture Science, Beijing 100081, China
| | - Stephen Obol Opiyo
- Molecular and Cellular Imaging Center - Columbus, Ohio Agricultural Research and Development Center, Columbus, OH 43210, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48823, USA
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
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Zhao D, Ferguson AA, Jiang N. What makes up plant genomes: The vanishing line between transposable elements and genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:366-80. [PMID: 26709091 DOI: 10.1016/j.bbagrm.2015.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023]
Abstract
The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ann A Ferguson
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA.
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Gilbert DM, Bridges MC, Strother AE, Burckhalter CE, Burnette JM, Hancock CN. Precise repair of mPing excision sites is facilitated by target site duplication derived microhomology. Mob DNA 2015; 6:15. [PMID: 26347803 PMCID: PMC4561436 DOI: 10.1186/s13100-015-0046-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/28/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND A key difference between the Tourist and Stowaway families of miniature inverted repeat transposable elements (MITEs) is the manner in which their excision alters the genome. Upon excision, Stowaway-like MITEs and the associated Mariner elements usually leave behind a small duplication and short sequences from the end of the element. These small insertions or deletions known as "footprints" can potentially disrupt coding or regulatory sequences. In contrast, Tourist-like MITEs and the associated PIF/Pong/Harbinger elements generally excise precisely, returning the genome to its original state. The purpose of this study was to determine the mechanisms underlying these excision differences, including the role of the host DNA repair mechanisms. RESULTS The transposition of the Tourist-like element, mPing, and the Stowaway-like element, 14T32, were evaluated using yeast transposition assays. Assays performed in yeast strains lacking non-homologous end joining (NHEJ) enzymes indicated that the excision sites of both elements were primarily repaired by NHEJ. Altering the target site duplication (TSD) sequences that flank these elements reduced the transposition frequency. Using yeast strains with the ability to repair the excision site by homologous repair showed that some TSD changes disrupt excision of the element. Changing the ends of mPing to produce non-matching TSDs drastically reduced repair of the excision site and resulted in increased generation of footprints. CONCLUSIONS Together these results indicate that the difference in Tourist and Stowaway excision sites results from transposition mechanism characteristics. The TSDs of both elements play a role in element excision, but only the mPing TSDs actively participate in excision site repair. Our data suggests that Tourist-like elements excise with staggered cleavage of the TSDs, which provides microhomology that facilitates precise repair. This slight modification in the transposition mechanism results in more efficient repair of the double stranded break, and thus, may be less harmful to host genomes by disrupting fewer genes.
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Affiliation(s)
- David M Gilbert
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC 29801 USA
| | - M Catherine Bridges
- Present Address: Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425 USA
| | - Ashley E Strother
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC 29801 USA
| | - Courtney E Burckhalter
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC 29801 USA
| | - James M Burnette
- Present Address: College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA 92521 USA
| | - C Nathan Hancock
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC 29801 USA
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Fattash I, Lee CN, Mo K, Yang G. Efficient transposition of the youngest miniature inverted repeat transposable element family of yellow fever mosquito in yeast. FEBS J 2015; 282:1829-40. [PMID: 25754725 DOI: 10.1111/febs.13257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 02/13/2015] [Accepted: 03/04/2015] [Indexed: 01/16/2023]
Abstract
Miniature inverted repeat transposable elements (MITEs) are often the most numerous DNA transposons in plant and animal genomes. The dramatic amplification of MITE families during evolution is puzzling, because the transposase sources for the vast majority of MITE families are unknown. The yellow fever mosquito genome contains > 220-Mb MITE sequences; however, transposition activity has not been demonstrated for any of the MITE families. The Gnome elements are the youngest MITE family in this genome, with at least 116 identical copies. To test whether the putative autonomous element Ozma is capable of mobilizing Gnome and its two sibling MITEs, analyses were performed in a yeast transposition assay system. Whereas the wild-type transposase resulted in very low transposition activity, mutations in the region containing a putative nuclear export signal motif resulted in a dramatic (at least 4160-fold) increase in transposition frequency. We have also demonstrated that each residue of the novel DD37E motif is required for the activity of the Ozma transposase. Footprint sequences left at the donor sites suggest that the transposase may cleave between the second and the third nucleotides from the 5' ends of the elements. The excised elements reinsert specifically at dinucleotide 'TA', ~ 55% of them in yeast genes. The elements described in this article could potentially be useful as genetic tools for genetic manipulation of mosquitoes.
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Affiliation(s)
- Isam Fattash
- Department of Biology, University of Toronto Mississauga, ON, Canada
| | - Chia-Ni Lee
- Department of Biology, University of Toronto Mississauga, ON, Canada
| | - Kaiguo Mo
- Department of Biology, University of Toronto Mississauga, ON, Canada
| | - Guojun Yang
- Department of Biology, University of Toronto Mississauga, ON, Canada
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Mach J. Rice MULEs transpose in yeast. THE PLANT CELL 2015; 27:5-6. [PMID: 25596003 PMCID: PMC4330591 DOI: 10.1105/tpc.114.136143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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