Skip to main content
SpringerLink
Log in

Gene Tagging, Gene- and Enhancer-Trapping, and Full-Length cDNA Overexpression in Physcomitrella Patens

  • Chapter
New Frontiers in Bryology

Abstract

Physcomitrella (Physcomitrella patens) is a useful model in plant biology, because of its simpler morphology and development as compared with other multicellular model plants and its suitability for gene targeting. Physcomitrella has the highest homologous recombination rate of any green plant examined to date, which can be utilized for the highly reliable gene targeting technique. Recent technical advances in genome biology make Physcomitrella even more useful. A shuttle mutagenesis technique based on homologous recombination was used to generate a large number of insertional mutant lines, as well as gene-trap and enhance-trap lines. More than 12,000 gene-trap lines were collected and the trapped genes, which showed cell- or tissue-specific expression patterns, were successfully identified. High quality full-length cDNA resources were established from the haploid generation of Physcomitrella; these resources are useful for functional analyses of genes and their products. More than 40,000 cDNAs have been sequenced from the both ends, and over 100,000 ESTs are publicly available. Sequence comparisons between Arabidopsis (Arabidopsis thaliana) and Physcomitrella revealed that two thirds of Arabidopsis genes had homologs in Physcomitrella. Physcomitrella should therefore be useful for analyzing the detailed function of genes originally isolated in other plant models. We identified 300 candidates for moss transcripts that are absent in vascular plants, and which likely represent new genes in land plants. Analysis of these genes will provide further new genetic resources. An over-expression screening system for full-length cDNA has been established to screen genes involved in cell polarity initiation and for maintenance during protoplast regeneration.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Ashton. N.W., Boyd, P.J., Cove, D.J., and Knight, C. D. (1990) Protoplasts as tools in the study of moss development. In: Chopra, R.N.B. (Ed.) Bryophyte development: physiology and biochemistry, (pp. 1–16 ) CRC Press, Boca Raton, FL.

    Google Scholar 

  • Bannerjee, A.K. (1980) 5’-terminal cap structure in eukaryotic mRNAs. Micro. Rev. 44, 175–205 (1980).

    Google Scholar 

  • Bellen, H.J. (1999) Ten years of enhance detection: lessons from the fly. Plant Cell 11: 2271–2281

    PubMed  CAS  Google Scholar 

  • Benfey, P.N., Ren, L. and Chua, N.-H. (1989) The CaMV 35S enhancer contains at least two domains which can confer different developmental and tissue-specific expression patterns. EMBO J. 8, 2195–2202

    PubMed  CAS  Google Scholar 

  • Bolker, M., Bohnert, H.U., Braun, K.H., Gorl, J., and Kahmann R (1995) Tagging pathogenicity genes in ustilago-maydis by restriction enzyme-mediated integration (REMI). Mol. Gen. Genet. 248, 547–552

    Article  PubMed  CAS  Google Scholar 

  • Carninci, P., Kvam, C., Kitamura, A., Ohsumi, T., Okazaki, Y., Itoh, M., Kamiya, M., Shibata, K., Sasaki, N., Izawa, M., Muramatsu, M., Hayashizaki, Y., and Schneider, C. (1996) High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37, 327–336

    Article  PubMed  CAS  Google Scholar 

  • Carninci, P., Shibata, Y., Hayatsu, N., Sugahara, Y., Shibata, K., Itoh, M., Konno, H., Okazaki, Y., Muramatsu, M., and Hayashizaki, Y (2000) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10, 1617–1630

    Article  PubMed  CAS  Google Scholar 

  • Chiu, W.L., Niwa, Y., Zeng, W., Hirano, T., Kobayashi, H,, and Sheen J. (1996) Engineered GFP as a vital reporter in plants. Curr. Biol. 6, 325–330

    CAS  Google Scholar 

  • Cove, D.J. (2000) The generation and modification of cell polarity. J. Expt. Bot. 51, 831–838

    Article  CAS  Google Scholar 

  • Cove, D.J., and Knight, C.D. (1993) The moss Physcomitrella patens, a model system with potential for the study of plant reproduction. Plant Cell 5, 1483–1488

    PubMed  Google Scholar 

  • Cove, D.J., Knight, C.D., and Lamparter T. (1997) Mosses as model systems. Trends Plant Sci. 2, 99–105

    Article  Google Scholar 

  • Doonan, J.H., Cove, D.J., and Lloyd, C.W. (1988) Microtubules and microfilaments in tip growth: evidence that microtubules impose polarity on protonemal growth in Physcomitrella patens. J. Cell Sci. 89, 533–540

    Google Scholar 

  • Egener, T., Granado, J., Cuitton, M.-C., Hohe, A., Holtorf, H., Lucht J.M., Rensing, S.A., Schlink, K., Schulte, J., Schween G., Zimmermann, S., Duwenig, E., Rak, B., and Reski, R. (2002) High frequency of phenotypic deviations in Physcomitrella patens plants transformed with a gene-disruption library. BMC Plant Biol. 2, 1–9

    Article  Google Scholar 

  • Flavell, R.B. (1994) Inactivation of gene-expression in plants as a consequence of specific sequence duplication. Proceed. Natl. Acad. Sci. U.S.A. 91, 3490–3496

    Google Scholar 

  • Granado, J.D., Kertesz Chaloupkova, K., Aebi, M., and Kues U (1997) Restriction enzyme-mediated DNA integration in Coprinus cinereus. Mol. Gen. Genet. 256, 28–36

    Article  PubMed  CAS  Google Scholar 

  • Gu, H., Zou, Y.R., and Rajewsky K (1993) Independent control of immunoglobulin switch recombination

    Google Scholar 

  • at individual switch regions evidenced through cre-loxP-mediated gene targeting. Cell 73, 1155–1164 Hiwatashi, Y., Nishiyama, T., Fujita, T., and Hasebe M. (2001) Establishment of gene-trap and enhancertrap systems in the moss Physcomitrella patens. Plant J. 28, 105–116

    Google Scholar 

  • Jefferson, R.A., Kavanagh, T.A., and Bevan, M.W. (1987) GUS fusions: ß-glucuronidase as a sensitive and versatile gene marker in higher plants. EMBO J. 6, 3901–3907

    PubMed  CAS  Google Scholar 

  • Jeong, D.H., Kang, H.G., Moon, S., Han, J.J., Park, S., Lee, H.S., An, K.S., and An GH (2002) T-DNA insertional mutagenesis for activation tagging in rice. Plant Physiol. 130, 1636–1644

    Article  PubMed  CAS  Google Scholar 

  • Kawai, J.S.A., Shibata, K., Yoshino, M., Itoh, M., Ishii, Y., Arakawa, T., Hara, A., Fukunishi, Y., Konno, H., Adachi, J., Fukuda, S., Aizawa, K., Izawa, M., Nishi, K., Kiyosawa, H., Kondo, S., Yamanaka, I., Saito, T., Okazaki, Y., Gojobori, T., Bono, H., Kasukawa, T., Saito, R., Kadota, K., Matsuda, H., Ashburner, M., Batalov, S., Casavant, T., Fleischmann, W., Gaasterland, T., Gissi, C., King, B., Kochiwa, H., Kuehl, P., Lewis, S., Matsuo, Y., Nikaido, I., Pesole, G., Quackenbush, J., Schriml, L.M., Staubli, F., Suzuki, R., Tomita, M., Wagner, L., Washio, T., Sakai, K., Okido, T., Furuno, M., Aono, H., Baldarelli, R., Barsh, G., Blake, J., Boffelli, D., Bojunga, N., Carninci, P., de Bonaldo, M.F., Brownstein, M.J., Bult, C., Fletcher, C., Fujita, M., Gariboldi, M., Gustincich, S., Hill, D., Hofmann, M., Hume, D.A., Kamiya, M., Lee, N.H., Lyons, P., Marchionni, L., Mashima, J., Mazzarelli, J., Mombaerts, P., Nordone, P., Ring, B., Ringwald, M,, Rodriguez, I., Sakamoto, N., Sasaki, H., Sato, K., Schonbach, C., Seya, T., Shibata, Y., Storch, K.F., Suzuki, H., Toyo-oka, K., Wang, K.H., Weitz, C., Whittaker, C., Wilming, L., Wynshaw-Boris, A., Yoshida, K., Hasegawa, Y., Kawaji, H., Kohtsuki, S., and Hayashizaki, Y. (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409, 685–690

    Google Scholar 

  • Kenrick, P., and Crane PR (1997) The origin and early evolution of plants on land. Nature 389, 33–39 Kristiansen, T.Z., and Pandey, A. (2002) Resources for full-length cDNAs. Trends Biochem. Sci. 27, 266–267

    Google Scholar 

  • Kuspa, A., and Loomis, W.F. (1992) Tagging developmental genes in dictyostelium by restriction enzyme-mediated integration of plasmid DNA. Proc. Natl. Acad. Sci. U.S.A. 89, 8803–8807

    Article  PubMed  CAS  Google Scholar 

  • Lewin, B. (2000) Genes V II. Oxford University Press, Oxford

    Google Scholar 

  • Li, W., Wu, C., and Luo, C (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2, 150–174

    PubMed  Google Scholar 

  • Ligrone, R. (19896) Structure, development and cytochemistry of mucilage-secreting hairs in the moss Timmiella barbuloides (Brid.) Moenk. Annals Bot. 58, 559–568

    Google Scholar 

  • Loomis, W.F. (1996) Genetic networks that regulate development in Dictyostelium cells. Microbiol Rev. 60, 135–50

    PubMed  CAS  Google Scholar 

  • Machuka, J., Bashiardes, S., Ruben, E., Spooner, K., Cuming, A., Knight, C., and Cove D (1999) Sequence analysis of expressed sequence tags from an ABA-treated cDNA library identifies stress response genes in the moss Physcomitrella patens. Plant Cell Physiol. 40, 378–387

    Article  PubMed  CAS  Google Scholar 

  • Mathur, J., and Hulskamp, M. (2002) Microtubules and microfilaments in cell morphogenesis in higher plants. Curr. Biol. 12, R669 - R676

    Article  PubMed  CAS  Google Scholar 

  • Mullins, E.D., and Kang, S. (200 1) Transformation: a tool for studying fungal pathogens of plants. Cell. Mol. Life Sci. 58, 2043–2052

    Google Scholar 

  • Nishiyama, T., Fujita, T., Shin-I, T., Seki, M., Nishide, H., Uchiyama, I., Kamiya, A., Carninci, P., Hayashizaki, Y., Shinozaki, K., Kohara, Y., and Hasebe, M. (2003) Comparative genomics of the Physcomitrella gametophytic transcriptome and Arabidopsis genome: implication for the land plant evolution. Proc Natl Acad Sci U S A: in press

    Google Scholar 

  • Nishiyama, T., Hiwatashi, Y., Sakakibara, K., Kato, M., and Hasebe, M. (2000) Tagged mutagenesis and gene-trap in the moss, Physcomitrella patens by Shuttle mutagenesis. DNA Res. 7, 9–17

    Article  PubMed  CAS  Google Scholar 

  • Osato, N., Itoh, M., Konno, H., Kondo, S., Shibata, K., Carninci, P., Shiraki, T., Shinagawa, A., Arakawa, T., Kikuchi, S., Sato, K., Kawai, J., and Hayashizaki, Y. (2002) A computer-based method of selecting clones for a full-Length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs. Genome Res. 12, 1127–1134

    PubMed  CAS  Google Scholar 

  • Qing, T., Nicholas, J.U., and Jason, W.R. (2002) Arabidopsis SHY2/IAA3 inhibits auxin-regulated gene expression. Plant Cell 14, 301–319

    Article  Google Scholar 

  • Rensing, S.A., Rombauts, S., Van de Peer, Y., and Reski, R. (2002) Moss transcriptome and beyond. Trends Plant Sci. 7, 535–538

    Article  PubMed  CAS  Google Scholar 

  • Reski, R. (1998) Development, genetics and molecular biology of mosses. Botanica Acta 111, 1–15

    CAS  Google Scholar 

  • Reski, R., Reynolds, S., Wehe, M., Kleber-Janke, T., and Kruse, S. (1998) Moss (Physcomitrella patens) expressed sequence tags include several sequences which are novel for plants. Botanica Acta 111, 143–149

    CAS  Google Scholar 

  • Riggle, P.J., and Kumamoto, C.A. (1998) Genetic analysis in fungi using restriction-enzyme-mediated integration. Curr. Opin. Microbiol. 1, 395–399

    Article  PubMed  CAS  Google Scholar 

  • Ringli, C., Baumberger, N., Diet, A., Frey, B., and Keller, B. (2002) ACTIN2 is essential for bulge site selection and tip growth during root hair development of Arabidopsis. Plant Physiol. 129, 1464–1472

    Article  PubMed  CAS  Google Scholar 

  • Schaefer, D., Zrÿd, J-P., Knight, C.D., and Cove, D.J. (1991) Stable transformation of the moss Physcomitrella patens. Mol. Gen. Genet. 226, 418–424

    PubMed  CAS  Google Scholar 

  • Schaefer, D.G. (2002) A new moss genetics: Targeted mutagenesis in Physcomitrella patens. Annu. Rev. Plant Biol. 53, 477–501

    Article  PubMed  CAS  Google Scholar 

  • Schaefer, D.G., and Zrÿd, J-P. (1997) Efficient gene targeting in the moss Physcomitrella patens. Plant J. 11, 1195–1206

    Article  PubMed  CAS  Google Scholar 

  • Schiestl, R.H., and Petes, T.D. (1991) Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 88, 7585–7589

    Article  PubMed  CAS  Google Scholar 

  • Schmidt, W.M., and Mueller, M.W. (1999) CapSelect: a highly sensitive method for 5’ CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs. Nuc. Acids Res. 27, e31

    Google Scholar 

  • Schumaker, K.S., and Dietrich, M.A. (1998) Hormone-induced signaling during moss development. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49, 501–523

    Article  PubMed  CAS  Google Scholar 

  • Seifert, H.S., Chen, E.Y., So, M., and Heffron, F. (1986) Shuttle mutagenesis: A method of transposon mutagenesis for Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 83, 735–739

    Article  PubMed  CAS  Google Scholar 

  • Seifert, H.S., So, M., and Heffron, F. (1986) Shuttle mutagenesis: A method of introducing transposons into transformable organisms. In: Setlow JK, Hollaender A (eds) Genetic Engineering: Principles and methods, (pp. 123–133 ) Plenum Press, New York

    Google Scholar 

  • Seki, M., Carninci, P., Nishiyama, Y., Hayashizaki, Y., and Shinozaki, K. (1998) High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. Plant J. 15, 707–720

    Article  PubMed  CAS  Google Scholar 

  • Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., Muramatsu, M., Hayashizaki, Y., Kawai, J., Carninci, P., Itoh, M., Ishii, Y., Arakawa, T., Shibata, K., Shinagawa, A., and Shinozaki, K. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296, 141–145

    Article  PubMed  Google Scholar 

  • Springer, P.S. (2002) Gene traps: Tools for plant development and genomics. Plant Cell 12, 1007–1020 Stapleton, M., Liao, G., Brokstein, P., Hong, L., Carninci, P., Shiraki, T., Hayashizaki, Y., Champe, M.

    Google Scholar 

  • Pacleb, J., Wan, K., Yu, C., Carlson, J., George, R., Celniker, S., and Rubin, G.M. (2002) The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res. 12, 1294–1300

    Article  PubMed  Google Scholar 

  • Sundaresan, V,. Springer, P., Volpe, T., Haward, S., Jones, J.D.G., Dean, C., Ma, H., and Martienssen, R. (1995) Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9, 1797–1810

    Article  PubMed  CAS  Google Scholar 

  • Suzuki, H., Fukunishi, Y., Kagawa, I., Saito, R., Oda, H., Endo, T., Kondo, S., Bono, H., Okazaki, Y., and Hayashizaki, Y. (2001) Protein-protein interaction panel using mouse full-length cDNAs. Genome Res. 11, 1758–1765

    Article  PubMed  CAS  Google Scholar 

  • Suzuki, Y., Yamashita, R., Nakai, K., and Sugano, S. (2002) DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nuc. Acids Res. 30, 328–331

    Article  CAS  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815

    Article  Google Scholar 

  • Walden, R. (2002) T-DNA tagging in a genomics era. Crit. Rev. Plant Sci. 21, 143–165

    Article  CAS  Google Scholar 

  • Weigel, D., Ahn, J., Blazquez, M., Borevitz, J., Christensen, S., Fankhauser, C., Ferrandiz, C., Kardailsky, I., Malancharuvil, E., Neff, M., Nguyen, J., Sato, S., Wang, Z., Xia, Y., Dixon, R., Harrison, M., Lamb, C., Yanofsky, M., and Chory J. (2000) Activation tagging in Arabidopsis. Plant Physiol. 122, 1003–1013

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Institute for Basic Biology, Okazaki, 444-8585, Japan

    Tomomichi Fujita, Tomoaki Nishiyama, Yuji Hiwatashi & Mitsuyasu Hasebe

Authors
  1. Tomomichi Fujita
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tomoaki Nishiyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yuji Hiwatashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mitsuyasu Hasebe
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Southern Illinois University-Carbondale, Carbondale, USA

    Andrew J. Wood

  2. USDA-ARS, Lubbock, USA

    Melvin J. Oliver

  3. University of Leeds, Leeds, UK

    David J. Cove

  4. Washington University, St. Louis, USA

    David J. Cove

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Fujita, T., Nishiyama, T., Hiwatashi, Y., Hasebe, M. (2004). Gene Tagging, Gene- and Enhancer-Trapping, and Full-Length cDNA Overexpression in Physcomitrella Patens . In: Wood, A.J., Oliver, M.J., Cove, D.J. (eds) New Frontiers in Bryology. Springer, Dordrecht. https://doi.org/10.1007/978-0-306-48568-8_7

Download citation

  • DOI: https://doi.org/10.1007/978-0-306-48568-8_7

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-90-481-6569-8

  • Online ISBN: 978-0-306-48568-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation