A Rice Stowaway MITE for Gene Transfer in Yeast

Miniature inverted repeat transposable elements (MITEs) lack protein coding capacity and often share very limited sequence similarity with potential autonomous elements. Their capability of efficient transposition and dramatic amplification led to the proposition that MITEs are an untapped rich source of materials for transposable element (TE) based genetic tools. To test the concept of using MITE sequence in gene transfer, a rice Stowaway MITE previously shown to excise efficiently in yeast was engineered to carry cargo genes (neo and gfp) for delivery into the budding yeast genome. Efficient excision of the cargo gene cassettes was observed even though the excision frequency generally decreases with the increase of the cargo sizes. Excised elements insert into new genomic loci efficiently, with about 65% of the obtained insertion sites located in genes. Elements at the primary insertion sites can be remobilized, frequently resulting in copy number increase of the element. Surprisingly, the orientation of a cargo gene (neo) on a construct bearing dual reporter genes (gfp and neo) was found to have a dramatic effect on transposition frequency. These results demonstrated the concept that MITE sequences can be useful in engineering genetic tools to deliver cargo genes into eukaryotic genomes.

[1]  Masaki Momose,et al.  Miniature Inverted-Repeat Transposable Elements of Stowaway Are Active in Potato , 2010, Genetics.

[2]  S. Wessler,et al.  Tourist: a large family of small inverted repeat elements frequently associated with maize genes. , 1992, The Plant cell.

[3]  G. Rubin,et al.  Genetic transformation of Drosophila with transposable element vectors. , 1982, Science.

[4]  S. Wessler,et al.  Evaluation of Hbr (MITE) markers for assessment of genetic relationships among maize (Zea mays L.) inbred lines , 2002, Theoretical and Applied Genetics.

[5]  L. Du,et al.  A piggyBac transposon-based mutagenesis system for the fission yeast Schizosaccharomyces pombe , 2011, Nucleic acids research.

[6]  Sean R. Eddy,et al.  An active DNA transposon family in rice , 2003, Nature.

[7]  S. Beverley,et al.  Trans-kingdom transposition of the Drosophila element mariner within the protozoan Leishmania. , 1997, Science.

[8]  S. Beverley,et al.  cis and trans factors affecting Mos1 mariner evolution and transposition in vitro, and its potential for functional genomics. , 2000, Nucleic acids research.

[9]  T. Bureau,et al.  Inter-MITE polymorphisms (IMP): a high throughput transposon-based genome mapping and fingerprinting approach , 2001, Theoretical and Applied Genetics.

[10]  J. Way,et al.  Transposition of plasmid-borne Tn10 elements does not exhibit simple length-dependence. , 1985, Genetics.

[11]  Elena R. Lozovsky,et al.  Unexpected stability of mariner transgenes in Drosophila. , 2002, Genetics.

[12]  S. Wessler,et al.  Dramatic amplification of a rice transposable element during recent domestication , 2006, Proceedings of the National Academy of Sciences.

[13]  Guojun Yang,et al.  A Rice Tc1/Mariner-Like Element Transposes in Yeast , 2006, The Plant Cell Online.

[14]  B. Charrier,et al.  Bigfoot. a new family of MITE elements characterized from the Medicago genus. , 1999, The Plant journal : for cell and molecular biology.

[15]  M. Ikawa,et al.  Efficient chromosomal transposition of a Tc1/mariner- like transposon Sleeping Beauty in mice , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Kazuhiro Kikuchi,et al.  The plant MITE mPing is mobilized in anther culture , 2003, Nature.

[17]  Thierry Heidmann,et al.  LINE-mediated retrotransposition of marked Alu sequences , 2003, Nature Genetics.

[18]  Guojun Yang,et al.  Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITE , 2009, Science.

[19]  Beery Yaakov,et al.  Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution , 2012, Theoretical and Applied Genetics.

[20]  Cédric Feschotte,et al.  Genome-wide analysis of mariner-like transposable elements in rice reveals complex relationships with stowaway miniature inverted repeat transposable elements (MITEs). , 2003, Genetics.

[21]  T. Hall,et al.  Kiddo, a new transposable element family closely associated with rice genes , 2001, Molecular Genetics and Genomics.

[22]  John Carbon,et al.  Isolation of a yeast centromere and construction of functional small circular chromosomes , 1980, Nature.

[23]  B. Papp,et al.  The Ancient mariner Sails Again: Transposition of the Human Hsmar1 Element by a Reconstructed Transposase and Activities of the SETMAR Protein on Transposon Ends , 2007, Molecular and Cellular Biology.

[24]  S. Oliver,et al.  The yeast 2 μ plasmid: strategies for the survival of a selfish DNA , 1986, Molecular and General Genetics MGG.

[25]  D. Prasher,et al.  Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Guojun Yang,et al.  ATon, abundant novel nonautonomous mobile genetic elements in yellow fever mosquito (Aedes aegypti) , 2012, BMC Genomics.

[27]  T. Langdon,et al.  A high-copy-number CACTA family transposon in temperate grasses and cereals. , 2003, Genetics.

[28]  Guojun Yang,et al.  MDM-1 and MDM-2: Two Mutator-Derived MITE Families in Rice , 2003, Journal of Molecular Evolution.

[29]  G. Rubin,et al.  Transposition of cloned P elements into Drosophila germ line chromosomes. , 1982, Science.

[30]  Yutaka Okumoto,et al.  Mobilization of a transposon in the rice genome , 2003, Nature.

[31]  Cédric Feschotte,et al.  Miniature Inverted-repeat Transposable Elements (MITEs) and their Relationship with Established DNA Transposons , 2001 .

[32]  M. Daboussi,et al.  Transposon-tagging identifies novel pathogenicity genes in Fusarium graminearum. , 2008, Fungal genetics and biology : FG & B.

[33]  W. Reznikoff,et al.  DNA length, bending, and twisting constraints on IS50 transposition. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Min Han,et al.  Efficient Transposition of the piggyBac (PB) Transposon in Mammalian Cells and Mice , 2005, Cell.

[35]  Cédric Feschotte,et al.  Miniature Inverted-Repeat Transposable Elements and Their Relationship to Established DNA Transposons , 2002 .

[36]  Guojun Yang,et al.  Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana , 2007, Proceedings of the National Academy of Sciences.

[37]  Feng Zhang,et al.  The Rice Miniature Inverted Repeat Transposable Element mPing Is an Effective Insertional Mutagen in Soybean1[C][W][OA] , 2011, Plant Physiology.

[38]  F. Bushman,et al.  A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture , 2012, Proceedings of the National Academy of Sciences.

[39]  L. Mularoni,et al.  INAUGURAL ARTICLE by a Recently Elected Academy Member:DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo , 2010 .

[40]  K. Wittrup,et al.  An Integrating Vector for Tunable, High Copy, Stable Integration into the Dispersed Ty δ Sites of Saccharomyces cerevisiae , 1996, Biotechnology progress.

[41]  J. Carbon,et al.  Characterization of a yeast replication origin (ars2) and construction of stable minichromosomes containing cloned yeast centromere DNA (CEN3). , 1981, Gene.

[42]  Bao Liu,et al.  In planta mobilization of mPing and its putative autonomous element Pong in rice by hydrostatic pressurization. , 2006, Journal of experimental botany.

[43]  J. Dowling,et al.  Transposition of the mariner element from Drosophila mauritiana in zebrafish. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[44]  S. Oliver,et al.  The yeast 2 micron plasmid: strategies for the survival of a selfish DNA. , 1986, Molecular & general genetics : MGG.

[45]  H. Levin,et al.  The Hermes Transposon of Musca domestica Is an Efficient Tool for the Mutagenesis of Schizosaccharomyces pombe , 2007, Genetics.

[46]  A. Bradley,et al.  Chromosomal transposition of a Tc1/mariner-like element in mouse embryonic stem cells. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[47]  R. Plasterk,et al.  Regulated transposition of a fish transposon in the mouse germ line , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[48]  A. Abbott,et al.  High-oleate peanut mutants result from a MITE insertion into the FAD2 gene , 2004, Theoretical and Applied Genetics.

[49]  D. Galas,et al.  The transposition frequency of IS1-flanked transposons is a function of their size. , 1982, Journal of molecular biology.

[50]  D. Garfinkel,et al.  Transposon tagging using Ty elements in yeast. , 1988, Genetics.

[51]  M. Davis,et al.  Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ line , 2001, Nature.

[52]  C. Weil,et al.  Transposition of maize Ac/Ds transposable elements in the yeast Saccharomyces cerevisiae , 2000, Nature Genetics.

[53]  S. Wessler,et al.  P instability factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Beery Yaakov,et al.  Genome-Wide Analysis of Stowaway-Like MITEs in Wheat Reveals High Sequence Conservation, Gene Association, and Genomic Diversification1[C][W] , 2012, Plant Physiology.

[55]  K. Takeda,et al.  Genomic distribution of MITEs in barley determined by MITE-AFLP mapping. , 2006, Genome.

[56]  M. Batzer,et al.  Alu repeats and human genomic diversity , 2002, Nature Reviews Genetics.

[57]  W. L. Fangman,et al.  Replication of each copy of the yeast 2 micron DNA plasmid occurs during the S phase , 1979, Cell.