Different status of the gene for ribosomal protein S16 inthe chloroplast genome during evolution of the genus Arabidopsis and closely related species

Genes and Genetic Systems

Volumn 85, Issue 5, 2010, Pages 319-326

  Roy, Shradha ^a   Ueda, Minoru ^a,c   Kadowaki, Koh Ichi ^b   Tsutsumi, Nobuhiro ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

Brassicaceae; Gene substitution; Group II intron; Splicing

Indexed keywords

PROTEIN S 16; RIBOSOME PROTEIN; UNCLASSIFIED DRUG;

AETHIONEMA GRANDIFLORUM; ANGIOSPERM; ARABIDOPSIS; ARABIS HIRSUTA; ARTICLE; BRASSICACEAE; CHLOROPLAST; CONTROLLED STUDY; DRABA NEMOROSA; GENE FUNCTION; GENETIC ANALYSIS; LOBULARIA MARITIMA; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIMARABIDOPSIS PUMILA; PLANT GENETICS; PSEUDOGENE; RNA SPLICING; SPECIES DIFFERENCE;

ARABIDOPSIS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; GENES, PLANT; GENOME, CHLOROPLAST; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIBOSOMAL PROTEINS; RNA SPLICING; SEQUENCE ALIGNMENT;

AETHIONEMA GRANDIFLORUM; ARABIDOPSIS; ARABIDOPSIS ARENOSA; ARABIDOPSIS LYRATA; ARABIDOPSIS THALIANA; ARABIS HIRSUTA; BRASSICACEAE; CRUCIHIMALAYA LASIOCARPA; DRABA NEMOROSA; LOBULARIA MARITIMA; MAGNOLIOPHYTA; OLIMARABIDOPSIS PUMILA;

EID: 79951491482     PISSN: 13417568     EISSN: 18805779     Source Type: Journal    
DOI: 10.1266/ggs.85.319     Document Type: Article

References (46)

1. Asakura, Y., Bayraktar, O. A., and Barkan, A. (2008) Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts. RNA 14, 2319-2332.
2. Beilstein, M. A., Al-Shehbaz, I. A., and Kellogg, E. A. (2006) Brassicaceae phylogeny and trichome evolution. Am. J. Bot. 93, 607-619.
3. Brandvainl, Y., and Wade, M. J. (2009) The functional transfer of genes from the mitochondria to the nucleus: the effects of selection, mutation, population size and rate of self-fertilization. Genetics 182, 1129-1139.
4. Brandvain, Y., Barker, M. S., and Wade, M. J. (2007) Gene co-inheritance and gene transfer. Science 315, 1685.
5. Chen, Z. J. (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids.Annu. Rev. Plant Biol. 58, 377-406.
6. Choi, H. K., Kim, D., Uhm, T., Limpens, E., Lim, H., Mun, J. H., Kalo, P., Penmetsa, R. V., Seres, A., Kulikova, O., et al. (2004) A sequence-based genetic map of Medicago truncatulaand comparison of marker colinearity with M. sativa.Genetics 166, 1463-1502.
7. Clauss, M. J., and Koch, M. A. (2006) Poorly known relatives of Arabidopsis thaliana. Trends Plant Sci. 11, 449-459.
8. Cusack, B. P., and Wolfe, K. H. (2007) When gene marriages don't work out: divorce by subfunctionalization. Trends Genet. 23, 270-272.
9. Doyle, J. J., Doyle, J. L., and Palmer, J. D. (1995) Multiple independent losses of two genes and one intron from legume chloroplast genomes. Syst. Bot. 20, 272-294.
10. Ford, M. A., and Kay, Q. O. N. (1985) The genetics of incompatibility in Sinapis arvensis L. Heredity 54, 99-102.
11. Gray, M. W. (1992) The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141, 233-357.
12. Guo, X., Castillo-Ramirez, S., Gonzalez, V., Bustos, P., Fernandez-Vazquez, J. L., Santamaria, R. I., Arellano, J., Cevallos, M. A., and Davila, G. (2007) Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts. BMC Genomics 8, 228.
13. Hall, A. E., Fiebig, A., and Preuss, D. (2002) Beyond the Arabidopsis genome: opportunities for comparative genomics.Plant Physiol. 129, 1439-1447.
14. Held, W. A., and Nomura, M. (1975) Escherichia coli 30 S ribosomal proteins uniquely required for assembly. J. Biol. Chem. 250, 3179-3184.
15. Hintz, M., Bartholmes, C., Nutt, P., Ziermann, J., Hameister, S., Neuffer, B., and Theissen, G. (2006) Catching a 'hopeful monster': shepherd's purse (Capsella bursa-pastoris) as a model system to study the evolution of flower development.J. Exp. Bot. 57, 3531-3542.
16. Jansen, R. K., Wojciechowski, M. F., Sanniyasi, E., Lee, S. B., and Daniell, H. (2008) Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). Mol. Phylogenet. Evol. 48, 1204-1217.
17. Kahlau, S., Aspinall, S., Gray, J. C., and Bock, R. (2006) Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J. Mol. Evol. 63, 194-207.
18. Khan, S., Wani, M. R., and Parveen, K. (2004) Induced genetic variability for quantitative traits in Vigna radiata (L.) Wilczek Pak. J. Bot. 36, 845-850.
19. Koch, M. A., Haubold, B., and Mitchell-Olds, T. (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 17, 1483-1498.
20. Kroeger, T. S., Watkins, K. P., Friso, G., Van Wijk, K. J., and Barkan, A. (2009) A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing. Proc. Natl. Acad. Sci. USA 106, 4537-4542.
21. Lehmann, K., and Schmidt, U. (2003) Group II introns: structure and catalytic versatility of large natural ribozymes.Crit. Rev. Biochem. Mol. Biol. 38, 249-303.
22. Lemen, C. (1980) Allocation of reproductive effort to the male and female strategies in wind-pollinated plants. Oecologia 45, 156-159.
23. Manton, I. (1935) The cytological history of Watercress (Nasturtium officinale R. Br.). Mol. Gen. Genet. 69, 132-157.
24. Melzer, S., Majewski, D. M., and Apel, K. (1990) Early changes in gene expression during the transition from vegetative to generative growth in the long-day plant Sinapis alba. Plant Cell 2, 953-961.
25. Michel, F., and Ferat, J. L. (1995) Structure and activities of group II introns. Annu. Rev. Biochem. 64, 435-461.
26. Michel, F., Umesono, K., and Ozeki, H. (1989) Comparative and functional anatomy of group II catalytic introns--a review.Gene 82, 5-30.
27. Millen, R. S., Olmstead, R. G., Adams, K. L., Palmer, J. D., Lao, N. T., Heggie, L., Kavanagh, T. A., Hibberd, J. M., Gray, J. C., Morden, C. W., et al. (2001) Many parallel losses of infAfrom chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13, 645-658.
28. Mitchell-Olds, T., Al-Shehbaz, I. A., Koch, M., and Sharbel, T. F. (2005) Crucifer evolution in the post-genomic era. In: Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants (ed.: Henry, R. J.), pp. 119-137. CAB International, Oxfordshire, UK.
29. Neuhaus, H., Scholz, A., and Link, G. (1989) Structure and expression of a split chloroplast gene from mustard (Sinapis alba): ribosomal protein gene rps16 reveals unusual transcriptional features and complex RNA maturation. Curr. Genet. 15, 63-70.
30. Okamoto, S., Odashima, M., Fujimoto, R., Sato, Y., Kitashiba, H., and Nishio, T. (2007) Self-compatibility in Brassica napus is caused by independent mutations in S-locus genes. Plant J. 50, 391-400.
31. Okumura, S., Sawada, M., Park, Y. W., Hayashi, T., Shimamura, M., Takase, H., and Tomizawa, K. (2006) Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts. Transgenic Res. 15, 637-646.
32. Persson, B. C., Bylund, G. O., Berg, D. E., and Wikstrom, P. M. (1995) Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics. J. Bacteriol. 177, 5554-5560.
33. Picóa, F. X., and Retana, J. (2001) The flowering pattern of the perennial herb Lobularia maritima: an unusual case in the Mediterranean basin. Acta Oecol-Int. J. Ecol. 22, 209-217.
34. Rand, D. M., Haney, R. A., and Fry, A. J. (2004) Cytonuclear coevolution: the genomics of cooperation. Trends Ecol. Evol. 19, 645-653.
35. Sampson, D. R. (1967) Frequency and distribution of self-incompatibility alleles in Raphanus raphanistrum. Genetics 56, 241-251.
36. Saski, C., Lee, S. B., Daniell, H., Wood, T. C., Tomkins, J., Kim, H. G., and Jansen, R. K. (2005) Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol. Biol. 59, 309-322.
37. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., and Tabata, S. (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6, 283-290.
38. Steane, D. A. (2005) Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae). DNA Res. 12, 215-220.
39. Tague, B. W. (2001) Germ-line transformation of Arabidopsis lasiocarpa. Transgenic Res. 10, 259-267.
40. Tangphatsornruang, S., Sangsrakru, D., Chanprasert, J., Uthaipaisanwong, P., Yoocha, T., Jomchai, N., and Tragoonrung, S. (2010) The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: Structural organization and phylogenetic relationships. DNA Res. 17, 11-22.
41. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
42. Timmis, J. N., Ayliffe, M. A., Huang, C. Y., and Martin, W. (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5, 123-135.
43. Toker, C., Canci, H., and Ceylan, F. O. (2006) Estimation of outcrossing rate in chickpea (Cicer Arietinum L.) sown in autumn. Euphytica 151, 201-205.
44. Ueda, M., Fujimoto, M., Arimura, S., Murata, J., Tsutsumi, N., and Kadowaki, K. (2007) Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus.Gene 402, 51-56.
45. Ueda, M., Nishikawa, T., Fujimoto, M., Takanashi, H., Arimura, S., Tsutsumi, N., and Kadowaki, K. (2008) Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal. Mol. Biol. Evol. 25, 1566-1575.
46. Wade, M. J., and Goodnight, C. J. (2006) Cyto-nuclear epistasis: two-locus random genetic drift in hermaphroditic and dioecious species. Evolution 60, 643-659.