Comparison of the transcript profiles from the root and the nodulating root of the model legume Lotus japonicus by serial analysis of gene expression

Molecular Plant-Microbe Interactions

Volumn 18, Issue 5, 2005, Pages 487-498

  Asamizu, Erika ^a   Nakamura, Yasukazu ^a   Sato, Shusei ^a   Tabata, Satoshi ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

Author keywords

RT PCR; Transcriptome

Indexed keywords

ARTICLE; COMPARATIVE STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC TRANSCRIPTION; LOTUS; METABOLISM; MICROBIOLOGY; NITROGEN FIXATION; PHYSIOLOGY; PLANT ROOT; RHIZOBIACEAE; SYMBIOSIS;

EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; LOTUS; NITROGEN FIXATION; PLANT ROOTS; RHIZOBIACEAE; SYMBIOSIS; TRANSCRIPTION, GENETIC;

LOTUS CORNICULATUS VAR. JAPONICUS; SALVIA;

EID: 17644371012     PISSN: 08940282     EISSN: None     Source Type: Journal    
DOI: 10.1094/MPMI-18-0487     Document Type: Article

References (58)

1. Asamizu, E., Nakamura, Y., Sato, S., and Tabata, S. 2000. Generation of 7137 non-redundant expressed sequence tags from a legume. Lotus japonicus. DNA Res. 7:127-130.
2. Asamizu, E., Kato, T., Sato, S., Nakamura, Y., Kaneko, T., and Tabata, S. 2003. Structural analysis of a Lotus japonicus Genome. IV. sequence features and mapping of seventy-three TAC clones which cover the 7.5 Mb regions of the genome. DNA Res. 10:115-122.
3. Asamizu, E., Nakamura, Y., Sato, S., and Tabata, S. 2004. Characteristics of the Lotus japonicus gene repertoire deduced from large-scale expressed sequence tag (EST) analysis. Plant Mol. Biol. 54:405-414.
4. Carmichael, G. G. 2003. Antisense starts making more sense. Nat. Biotechnol. 21:371-372.
5. Colebatch, G., Kloska, S., Trevaskis, B., Freund, S., Altmann, T., and Udvardi, M. K. 2002. Novel aspects of symbiotic nitrogen fixation uncovered by transcript profiling with cDNA arrays. Mol. Plant Microbe-Interact. 15:411-420.
6. Colebatch, G., Desbrosses, G., Ott, T., Krusell, L., Montanari, O., Kloska, S., Kopka, J., and Udvardi, M. K. 2004. Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. Plant J. 39:487-512.
7. Ekman, D. R., Lorenz, W. W., Przybyla, A. E., Wolfe, N. L., and Dean, J. F. 2003. SAGE analysis of transcriptome responses in Arabidopsis roots exposed to 2,4,6-trinitrotoluene. Plant Physiol. 133:1397-1406.
8. Endo, M., Kokubun, T., Takahata, Y., Higashitani, A., Tabata, S., and Watanabe, M. 2000. Analysis of expressed sequence tags of flower buds in Lotus japonicus. DNA Res. 7:213-216.
9. Endo, M., Hakozaki, H., Kokubun, T., Masuko, H., Takahata, Y., Tsuchiya, T., Higashitani, A., Tabata, S., and Watanabe, M. 2002a. Generation of 919 expressed sequence tags from immature flower buds and gene expression analysis using expressed sequence tags in the model plant Lotus japonicus. Genes Genet. Syst. 77:277-282.
10. Endo, M., Matsubara, H., Kokubun, T., Masuko, H., Takahata, Y., Tsuchiya, T., Fukuda, H., Demura, T., and Watanabe, M. 2002b. The advantages of cDNA microarray as an effective tool for identification of reproductive organ-specific genes in a model legume. Lotus japonicus. FEBS (Fed. Eur. Biochem. Soc.) Lett. 514:229-37.
11. Endre, G., Kereszt, A., Kevei, Z., Mihacea, S., Kalo, P., and Kiss, G. B. 2002. A receptor kinase gene regulating symbiotic nodule development. Nature 417:962-966.
12. Fizames, C., Munos, S., Cazettes, C., Nacry, P., Boucherez, J., Gaymard, F., Piquemal, D., Delorme, V., Commes, T., Doumas, P., Cooke, R., Marti, J., Sentenae, H., and Gojon, A. 2004. The Arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence. Plant Physiol. 134:67-80.
13. Handberg, K., and Stougaard, J. 1992. Lotus japonicus, an autogamous, diploid legume species for classical and molecular genetics. Plant J. 2:487-496.
14. Hayashi, M., Miyahara, A., Sato, S., Kato, T., Yoshikawa, M., Taketa, M., Hayashi, M., Pedrosa, A., Onda, R., Imaizumi-Anraku, H., Bachmair, A., Sandal, N., Stougaard, J., Murooka, Y., Tabata, S., Kawasaki, S., Kawaguchi, M., and Harada, K. 2001. Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population. DNA Res. 8:301-310.
15. 3 inhibition on root hair deformation. Mol. Plant Microbe Interact. 10:215-220.
16. Imaizumi-Anraku, H., Kawaguchi, M., Koiwa, H., Akao, S., and Syono, K. 1997. Two ineffective-nodulating mutants of Lotus japonicus - Different phenotypes caused by the blockage of endocytotic bacterial release and nodule mutation. Plant Cell Physiol. 38:871-881.
17. Ito, M., Miyamoto, J., Mori, Y., Fujimoto, S., Uchiumi, T., Abe, M., Suzuki, A., Tabata, S., and Fukui, K. 2000. Genome and chromosome dimensions of Lotus japonicus. J. Plant Res. 113:435-442.
18. Jones, S. J., Riddle, D. L., Pouzyrev, A. T., Velculescu, V. E., Hillier, L., Eddy, S. R., Stricklin, S. L., Baillie, D. L., Waterston, R., and Marra, M. A. 2001. Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res. 11:1349-1352.
19. Jung, S. H., Lee, J. Y., and Lee, D. H. 2003. Use of SAGE technology to reveal changes in gene expression in Arabidopsis leaves undergoing cold stress. Plant Mol. Biol. 52:553-567.
20. Kapranov, P., Routt, S. M., Bankaitis, V. A., de Bruijn, F. J., Szczyglowski, K. 2001. Nodule-specific regulation of phosphatidylinositol transfer protein expression in Lotus japonicus. Plant Cell 13:1369-1382.
21. Kawaguchi, M. 2000. Lotus japonicus "Miyakojima" MG-20: An early flowering accession suitable for indoor handling. J. Plant Res. 113:507-509.
22. Kaneko, T., Asamizu, E., Kato, T., Sato, S., Nakamura, Y., and Tabata, S. 2003. Structural analysis of a Lotus japonicus genome. III. Sequence features and mapping of sixty-two TAC clones which cover the 6.7 Mb regions of the genome. DNA Res. 10:27-33.
23. Kato, T., Kaneko, T., Sato, S., Nakamura, Y., and Tabata, S. 2000. Complete structure of the chloroplast genome of a legume. Lotus japonicus. DNA Res. 7:323-330.
24. Kato, T., Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., and Tabata, S. 2003. Structural analysis of a Lotus japonicus Genome. V. Sequence features and mapping of sixty four TAC clones which cover the 6.4 Mb regions of the genome. DNA Res. 10:277-285.
25. Kistner, C., and Parniske, M. 2002. Evolution of signal transduction in intracellular symbiosis. Trends Plant Sci. 7:511-518.
26. Kouchi, H., Shimomura, K., Hata, S., Hirota, A., Wu, G. J., Kumagai, H., Tajima, S., Suganuma, N., Suzuki, A., Aoki, T., Hayashi, M., Yokoyama, T., Ohyama, T., Asamizu, E., Kuwata, C., Shibata, D., and Tabata, S. 2004. Large-scale analysis of gene expression profile during early stages of root nodule formation in a model legume, Lotus japonicus. DNA Res. 11:263-274.
27. Krusell, L., Madsen, L. H., Sato, S., Aubert, G., Genua, A., Szczyglowski, K., Duc, G., Kaneko, T., Tabata, S., de Bruijn, F., Pajuelo, E., Sandal, N., and Stougaard, J. 2002. Shoot control of root development and nodulation is mediated by a receptor-like kinase. Nature 420:422-426.
28. Laplaze, L., Gherbi, H., Duhoux, E., Pawlowski, K., Auguy, F., Guermache, F., Franche, C., and Bogusz, D. 2002. Symbiotic and non-symbiotic expression of cgMT1, a metallothionein-like gene from the actinorhizal tree Casuarina glauca. Plant Mol. Biol. 49:81-92.
29. Lee, J. Y., and Lee, D. H. 2003. Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiol. 132:517-529.
30. Martirani, L., Stiller, J., Mirabella, R., Alfano, F., Lamberti A, Radutoiu, S. E., Iaccarino, M., Gresshoff, P. M., and Chiurazzi, M. 1999. T-DNA tagging of nodulation- and root-related genes in Lotus japonicus: Expression patterns and potential for promoter trapping and insertional mutagenesis. Mol. Plant Microbe Interact. 12:275-284.
31. Matsumura, H., Nirasawa, S., and Terauchi, R. 1999. Technical advance: Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J. 20:719-726.
32. Matsumura, H., Nirasawa, S., Kiba, A., Urasaki, N., Saitoh, H., Ito, M., Kawai-Yamada, M., Uchimiya, H., and Terauchi, R. 2003a. Overexpression of Bax inhibitor suppresses the fungal elicitor-induced cell death in rice (Oryza sativa L) cells. Plant J. 33:425-434.
33. Matsumura, H., Reich, S., Ito, A., Saitoh, H., Kamoun, S., Winter, P., Kahl, G., Reuter, M., Kruger, D. H., and Terauchi, R. 2003b. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc. Natl. Acad. Sci. U.S.A. 100:15718-15723.
34. Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R. R., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S. E., Pagni, M., Peyruc, D., Ponting, C. P., Selengut, J. D., Servant, F., Sigrist, C. J. A., Vaughan, R., and Zdobnov, E. M. 2003. The InterPro database. 2003 brings increased coverage and new features. Nucleic Acids Res. 31:315-318.
35. Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Sato, S., and Tabata, S. 2002. Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5-mb regions of the genome. DNA Res. 9:63-70.
36. Nishimura, R., Hayashi, M., Wu, G. J., Kouchi, H., Imaizumi-Anraku, H., Murakami, Y., Kawasaki, S., Akao, S., Ohmori, M., Nagasawa, M., Harada, K., and Kawaguchi, M. 2002. HARI mediates systemic regulation of symbiotic organ development. Nature 420:426-429.
37. Patankar, S., Munasinghe, A., Shoaibi, A., Cummings, L. M., and Wirth, D. F. 2001. Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite. Mol. Biol. Cell 12:3114-3125.
38. Polyak, K., Xia, Y., Zweier, J. L., Kinzler, K. W., and Vogelstein, B. 1997. A model for p53 induced apoptosis. Nature 389:300-305.
39. Poulsen, C., and Podenphant, L. 2002. Expressed sequence tags from roots and nodule primordia of Lotus japonicus infected with Mesorhizobium loti. Mol. Plant Microbe Interact. 15:376-379.
40. Riely, B. K., Ane, J. M., Penmetsa, R. V., Cook, D. R. 2004. Genetic and genomic analysis in model legumes bring Nod-factor signaling to center stage. Curr. Opin. Plant Biol. 7:408-413.
41. Sandal, N., Krusell, L., Radutoiu, S., Olbryt, M., Pedrosa, A., Stracke, S., Sato, S., Kato, T., Tabata, S., Parniske, M., Bachmair, A., Ketelsen, T., and Stougaard, J. 2002. A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci. Genetics 161:1673-1683.
42. Sato, S., Kaneko, T., Nakamura, Y., Asamizu, E., Kato, T., and Tabata, S. 2001. Structural analysis of a Lotus japonicus genome. I. Sequence features and mapping of fifty-six TAC clones which cover the 5.4 mb regions of the genome. DNA Res. 8:311-318.
43. Schauser, L., Handberg, K., Sandal, N., Stiller, J., Thykjaer, T., Pajuelo, E., Nielsen, A., and Stougaard, J. 1998. Symbiotic mutants deficient in nodule establishment identified after T-DNA transformation of Lotus japonicus. Mol Gen Genet. 259:414-423.
44. Schauser, L., Roussis, A., Stiller, J., and Stougaard, J. 1999. A plant regulator controlling development of symbiotic root nodules. Nature 402:191-195.
45. Searle, I. R., Men, A. E., Laniya, T. S., Buzas, D. M., Iturbe-Ormaetxe, I., Carroll, B. J., and Gresshoff, P. M. 2003. Long-distance signaling in Modulation directed by a CLAVATA1-like receptor kinase. Science 299:109-112.
46. Stracke, S., Kistner, C., Yoshida, S., Mulder, L., Sato, S., Kaneko, T., Tabata, S., Sandal, N., Stougaard, J., Szczyglowski K., and Parniske, M. 2002. A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417:959-962.
47. Szczyglowski, K., Hamburger, D., Kapranov, P., and de Bruijn, F. J. 1997. Construction of a Lotus japonicus late nodulin expressed sequence tag library and identification of novel nodule-specific genes. Plant Physiol. 114:1335-1346.
48. Szczyglowski, K., Shaw, R. S., Wopereis, J., Copeland, S., Hamburger, D., Kasiborski, B., Dazzo, F. B., and de Bruijn, F. J. 1998. Nodule organogenesis and symbiotic mutants of the model legume Lotus japonicus. Mol. Plant Microbe Interact. 11:684-697.
49. Uchiumi, T., Shimoda, Y., Tsuruta, T., Mukoyoshi, Y., Suzuki, A., Senoo, K., Sato, S., Kato, T., Tabata, S., Higashi, S., and Abe, M. 2002. Expression of symbiotic and nonsymbiotic globin genes responding to microsymbionts on Lotus japonicus. Plant Cell Physiol. 43:1351-1358.
50. Velculescu, V. E., Zhang, L., Vogelstein, B., Kinzler, K. W. 1995. Serial analysis of gene expression. Science 270:484-487.
51. Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D. E. Jr., Hieter, P., Vogelstein, B., and Kinzler, K. W. 1997. Characterization of the yeast transcriptome. Cell 88:243-251.
52. Vicient, C. M., and Delseny, M. 1999. Isolation of total RNA from Arabidopsis thaliana seeds. Anal. Biochem. 268:412-413.
53. Webb, K. J., Skot, L., Nicholson, M. N., Jorgensen, B., and Mizen, S. 2000. Mesorhizobium loti increases root-specific expression of a calcium-binding protein homologue identified by promoter tagging in Lotus japonicus. Mol. Plant Microbe Interact. 13:606-616.
54. Wittenberg, J. B., Appleby, C. A., Bergersen, F. J., and Turner, G. L. 1975. Leghemoglobin: The role of hemoglobin in the nitrogen-fixing legume root nodule. Ann. N Y Acad. Sci. 244:28-34.
55. Yamada, K., Lim, J., Dale, J. M., Chen, H., Shinn, P., Palm, C. J., Southwick, A. M., Wu, H. C., Kim, C., Nguyen, M., Pham, P., Cheuk, R., Karlin-Newmann, G., Liu, S. X., Lam, E., Sakano, H., Wu, T., Yu, G., Miranda, M., Quach, H. L., Tripp, M., Chang, C. H., Lee, J. M., Toriumi, M., Chan, M. M., Tang, C. C., Onodera, C. S., Deng, J. M., Akiyama, K., Ansari, Y., Arakawa, T., Banh, J., Banno, F., Bowser, L., Brooks, S., Carninci, P., Chao, Q., Choy, N., Enju, A., Goldsmith, A. D., Gurjal, M., Hansen, N. F., Hayashizaki, Y., Johnson-Hopson, C., Hsuan, V. W., Iida, K., Karnes, M., Khan, S., Koesema, E., Ishida, J., Jiang, P. X., Jones, T., Kawai, J., Kamiya, A., Meyers, C., Nakajima, M., Narusaka, M., Seki, M., Sakurai, T., Satou, M., Tamse, R., Vaysberg, M., Wallender, E. K., Wong, C., Yamamura, Y., Yuan, S., Shinozaki, K., Davis, R. W., Theologis, A., and Ecker, J. R. 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842-846.
56. Yelin, R., Dahary, D., Sorek, R., Levanon, E. Y., Goldstein, O., Shoshan, A., Diber, A., Biton, S., Tamir, Y., Khosravi, R., Nemzer, S., Pinner, E., Walach, S., Bernstein, J., Savitsky, K., and Rotman, G. 2003. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21:379-386.
57. Yu, J., Zhang, L., Hwang, P. M., Rago, C., Kinzler, K. W., and Vogelstein, B. 1999. Identification and classification of p53-regulated genes. Proc. Natl. Acad. Sci. U.S.A. 96:14517-14522.
58. Zhang, L., Zhou, W., Velculescu, V. E., Kern, S. E., Hruban, R. H., Hamilton, S. R., Vogelstein, B., and Kinzler, K. W. 1997. Gene expression profiles in normal and cancer cells. Science 276:1268-1272.