Functional evolution of phosphatidylethanolamine binding proteins in soybean and arabidopsis

Plant Cell

Volumn 27, Issue 2, 2015, Pages 323-336

  Wang, Zheng ^a   Zhou, Zhengkui ^a   Liu, Yunfeng ^b   Liua, Tengfei ^a,c   Li, Qing ^a,c   Ji, Yuanyuan ^a,c   Li, Congcong ^a,c   Fang, Chao ^a,c   Wang, Min ^c   Wu, Mian ^a   Shen, Yanting ^a,c   Tang, Tian ^d   Jianxin, M ^a   Tian, Zhixi ^a  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b PURDUE UNIVERSITY   (United States)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; GLYCINE MAX; MAGNOLIOPHYTA;

AMINO ACID; PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN; PROTEIN BINDING; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARABIDOPSIS; CELL FRACTIONATION; CHEMISTRY; DUPLICATE GENE; FLOWER; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYSIOLOGY; PLANT GENE; PROTEIN TRANSPORT; SOYBEAN;

AMINO ACID SEQUENCE; AMINO ACIDS; ARABIDOPSIS; EVOLUTION, MOLECULAR; FLOWERS; GENE EXPRESSION REGULATION, PLANT; GENES, DUPLICATE; GENES, PLANT; MOLECULAR SEQUENCE DATA; PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN; PLANT PROTEINS; PROTEIN BINDING; PROTEIN TRANSPORT; SOYBEANS; SUBCELLULAR FRACTIONS;

EID: 84924292510     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.114.135103     Document Type: Article

References (59)

1. Abe, M., Kobayashi, Y., Yamamoto, S., Daimon, Y., Yamaguchi, A., Ikeda, Y., Ichinoki, H., Notaguchi, M., Goto, K., and Araki, T. (2005). FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science 10. 309: 1052-1056.
2. Adams, K.L., and Wendel, J.F. (2005). Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 10. 8: 135-141.
3. Adrian, J., Farrona, S., Reimer, J.J., Albani, M.C., Coupland, G., and Turck, F. (2010). cis-Regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis. Plant Cell 10. 22: 1425-1440.
4. Ahn, J.H., Miller, D., Winter, V.J., Banfi10. eld, M.J., Lee, J.H., Yoo, S.Y., Henz, S.R., Brady, R.L., and Weigel, D. (2006). A divergent external loop confers antagonistic activity on floral regulators FT and TFL1. EMBO J. 10. 25: 605-614.
5. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 10. 215: 403-410.
6. Banfi10. eld, M.J., Barker, J.J., Perry, A.C., and Brady, R.L. (1998). Function from structure? The crystal structure of human phosphatidylethanolamine- binding protein suggests a role in membrane signal transduction. Structure 10. 6: 1245-1254.
7. Blanc, G., Hokamp, K., and Wolfe, K.H. (2003). A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 10. 13: 137-144.
8. Bowers, J.E., Chapman, B.A., Rong, J., and Paterson, A.H. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 10. 422: 433-438.
9. Bradley, D., Ratcliffe, O., Vincent, C., Carpenter, R., and Coen, E. (1997). Inflorescence commitment and architecture in Arabidopsis. Science 10. 275: 80-83.
10. Capella-Gutiérrez, S., Silla-Martínez, J.M., and Gabaldón, T. (2009). trimAl: a tool for automated alignment trimming in largescale phylogenetic analyses. Bioinformatics 10. 25: 1972-1973.
11. Carmona, M.J., Calonje, M., and Martínez-Zapater, J.M. (2007). The FT/TFL1 gene family in grapevine. Plant Mol. Biol. 10. 63: 637-650.
12. Chung, K.S., Yoo, S.Y., Yoo, S.J., Lee, J.S., and Ahn, J.H. (2010). BROTHER OF FT AND TFL1 (BFT), a member of the FT/TFL1 family, shows distinct pattern of expression during the vegetative growth of Arabidopsis. Plant Signal. Behav. 10. 5: 1102-1104.
13. Clough, S.J., and Bent, A.F. (1998). Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 10. 16: 735-743.
14. Conant, G.C., and Wolfe, K.H. (2008). Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet. 10. 9: 938-950.
15. Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I., Giakountis, A., Farrona, S., Gissot, L., Turnbull, C., and Coupland, G. (2007). FT protein movement contributes to longdistance signaling in floral induction of Arabidopsis. Science 10. 316: 1030-1033.
16. Danilevskaya, O.N., Meng, X., Hou, Z., Ananiev, E.V., and Simmons, C.R. (2008). A genomic and expression compendium of the expanded PEBP gene family from maize. Plant Physiol. 10. 146: 250-264.
17. Du, J., Tian, Z., Sui, Y., Zhao, M., Song, Q., Cannon, S.B., Cregan, P., andMa, J. (2012). Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean. Plant Cell 10. 24: 21-32.
18. Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 10. 32: 1792- 1797.
19. Flagel, L.E., and Wendel, J.F. (2009). Gene duplication and evolutionary novelty in plants. New Phytol. 10. 183: 557-564.
20. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., and Postlethwait, J. (1999). Preservation of duplicate genes by complementary, degenerative mutations. Genetics 10. 151: 1531-1545.
21. Freeling, M. (2009). Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 10. 60: 433-453.
22. Gill, N., Findley, S., Walling, J.G., Hans, C., Ma, J., Doyle, J., Stacey, G., and Jackson, S.A. (2009). Molecular and chromosomal evidence for allopolyploidy in soybean. Plant Physiol. 10. 151: 1167- 1174.
23. Hanano, S., and Goto, K. (2011). Arabidopsis TERMINAL FLOWER1 is involved in the regulation of flowering time and inflorescence development through transcriptional repression. Plant Cell 10. 23: 3172-3184.
24. Hanzawa, Y., Money, T., and Bradley, D. (2005). A single amino acid converts a repressor to an activator of flowering. Proc. Natl. Acad. Sci. USA 10. 102: 7748-7753.
25. Hedman, H., Källman, T., and Lagercrantz, U. (2009). Early evolution of the MFT-like gene family in plants. Plant Mol. Biol. 10. 70: 359-369.
26. Hengst, U., Albrecht, H., Hess, D., and Monard, D. (2001). The phosphatidylethanolamine-binding protein is the prototype of a novel family of serine protease inhibitors. J. Biol. Chem. 10. 276: 535- 540.
27. Ho, W.W., and Weigel, D. (2014). Structural features determining flower-promoting activity of Arabidopsis FLOWERING LOCUS T. Plant Cell 10. 26: 552-564.
28. Hughes, A.L. (1994). The evolution of functionally novel proteins after gene duplication. Proc. Biol. Sci. 10. 256: 119-124.
29. Innan, H., and Kondrashov, F. (2010). The evolution of gene duplications: classifying and distinguishing between models. Nat. Rev. Genet. 10. 11: 97-108.
30. Jaillon, O., et al.; French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 10. 449: 463-467.
31. James, L.C., and Tawfi10. k, D.S. (2003). Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem. Sci. 10. 28: 361-368.
32. Jiao, Y., et al. (2011). Ancestral polyploidy in seed plants and angiosperms. Nature 10. 473: 97-100.
33. Jung, C.H., Wong, C.E., Singh, M.B., and Bhalla, P.L. (2012). Comparative genomic analysis of soybean flowering genes. PLoS ONE 10. 7: e38250.
34. Kardailsky, I., Shukla, V.K., Ahn, J.H., Dagenais, N., Christensen, S.K., Nguyen, J.T., Chory, J., Harrison, M.J., and Weigel, D. (1999). Activation tagging of the floral inducer FT. Science 10. 286: 1962-1965.
35. Karlgren, A., Gyllenstrand, N., Källman, T., Sundström, J.F., Moore, D., Lascoux, M., and Lagercrantz, U. (2011). Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiol. 10. 156: 1967-1977.
36. Kaufmann, K., Wellmer, F., Muiño, J.M., Ferrier, T., Wuest, S.E., Kumar, V., Serrano-Mislata, A., Madueño, F., Krajewski, P., Meyerowitz, E.M., Angenent, G.C., and Riechmann, J.L. (2010). Orchestration of floral initiation by APETALA1. Science 10. 328: 85-89.
37. Kobayashi, Y., Kaya, H., Goto, K., Iwabuchi, M., and Araki, T. (1999). A pair of related genes with antagonistic roles in mediating flowering signals. Science 10. 286: 1960-1962.
38. Kondrashov, F.A., Rogozin, I.B., Wolf, Y.I., and Koonin, E.V. (2002). Selection in the evolution of gene duplications. Genome Biol. 10. 3: RESEARCH0008.
39. Mimida, N., Goto, K., Kobayashi, Y., Araki, T., Ahn, J.H., Weigel, D., Murata, M., Motoyoshi, F., and Sakamoto, W. (2001). Functional divergence of the TFL1-like gene family in Arabidopsis revealed by characterization of a novel homologue. Genes Cells 10. 6: 327-336.
40. Oakley, T.H., Ostman, B., and Wilson, A.C. (2006). Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes. Proc. Natl. Acad. Sci. USA 10. 103: 11637-11641.
41. Ohno, S. (1970). Evolution by Gene Duplication. (New York: Springer).
42. Papp, B., Pál, C., and Hurst, L.D. (2003). Dosage sensitivity and the evolution of gene families in yeast. Nature 10. 424: 194-197.
43. Ramsey, J., and Schemske, D. (1998). Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst. 10. 29: 467-501.
44. Schlueter, J.A., Lin, J.Y., Schlueter, S.D., Vasylenko-Sanders, I.F., Deshpande, S., Yi, J., O'10. Bleness, M., Roe, B.A., Nelson, R.T., Scheffl10. er, B.E., Jackson, S.A., and Shoemaker, R.C. (2007). Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics 10. 8: 330.
45. Schmutz, J., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature 10. 463: 178-183.
46. Sémon, M., and Wolfe, K.H. (2007). Consequences of genome duplication. Curr. Opin. Genet. Dev. 10. 17: 505-512.
47. Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 10. 30: 1312-1313.
48. Tian, Z., Wang, X., Lee, R., Li, Y., Specht, J.E., Nelson, R.L., McClean, P.E., Qiu, L., and Ma, J. (2010). Artificial selection for determinate growth habit in soybean. Proc. Natl. Acad. Sci. USA 107: 8563-8568.
49. Veitia, R.A., Bottani, S., and Birchler, J.A. (2008). Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends Genet. 10. 24: 390-397.
50. Wang, Y., Wang, X., and Paterson, A.H. (2012). Genome and gene duplications and gene expression divergence: a view from plants. Ann. N. Y. Acad. Sci. 10. 1256: 1-14.
51. Wendel, J.F. (2000). Genome evolution in polyploids. Plant Mol. Biol. 42: 225-249.
52. Wigge, P.A., Kim, M.C., Jaeger, K.E., Busch, W., Schmid, M., Lohmann, J.U., and Weigel, D. (2005). Integration of spatial and temporal information during floral induction in Arabidopsis. Science 309: 1056-1059.
53. Xi, W., Liu, C., Hou, X., and Yu, H. (2010). MOTHER OF FT AND TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis. Plant Cell 10. 22: 1733-1748.
54. Yamaguchi, A., Kobayashi, Y., Goto, K., Abe, M., and Araki, T. (2005). TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT. Plant Cell Physiol. 10. 46: 1175-1189.
55. Yang, Z. (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 10. 13: 555-556.
56. Yoo, S.D., Cho, Y.H., and Sheen, J. (2007). Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 10. 2: 1565-1572.
57. Yoo, S.J., Chung, K.S., Jung, S.H., Yoo, S.Y., Lee, J.S., and Ahn, J.H. (2010). BROTHER OF FT AND TFL1 (BFT) has TFL1-like activity and functions redundantly with TFL1 in inflorescence meristem development in Arabidopsis. Plant J. 10. 63: 241-253.
58. Yoo, S.Y., Kardailsky, I., Lee, J.S.,Weigel, D., and Ahn, J.H. (2004). Acceleration of flowering by overexpression of MFT (MOTHER OF FT AND TFL1). Mol. Cells 10. 17: 95-101.
59. Zhang, J., Rosenberg, H.F., and Nei, M. (1998). Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 10. 95: 3708-3713.