Vascular gene expression: A hypothesis

Frontiers in Plant Science

Volumn 4, Issue JUL, 2013, Pages

  Martínez Navarro, Angélica C ^a   Galván Gordillo, Santiago V ^a   Xoconostle Cázares, Beatriz ^a   Ruiz Medrano, Roberto ^a  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

Author keywords

Companion cell; Evolution; Phloem; Sieve element; Vascular tissue

Indexed keywords

EID: 84899769297     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2013.00261     Document Type: Article

References (50)

1. Bailey, T. L., and Elkan, C. (1994). "Fitting a mixture model by expectation maximization to discover motifs in biopolymers, " in Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, (Menlo Park, CA: AAAI Press), 28-36.
2. Banks, J. A., Nishiyama, T., Hasebe, T., Bowman, J. M., Gribskov, M., dePamphilis, C., et al. (2011). The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332, 960-963. doi: 10.1126/science.1203810
3. Becker, B., and Marin, B. (2009). Streptophyte algae and the origin of embryophytes. Ann. Bot. 103, 999-1004. doi: 10.1093/aob/mcp044
4. Bergmann, D., Lukowitz, W., and Somerville, C. (2004). Stomatal development and pattern controlled by a MAPKK kinase. Science 304, 1494-1497. doi: 10.1126/science.1096014
5. Bonke, M., Thitamadee, S., Mähönen, A., Hauser, M.-T., and Helariutta, Y. (2003). APL regulates vascular tissue identity in Arabidopsis. Nature 426, 181-186. doi: 10.1038/nature02100
6. Burr, F. A., and Evert, R. F. (1973). Some aspects of sieve-element structure and development in Selaginella kraussiana. Protoplasma 78, 81-97. doi: 10.1007/BF01281524
7. Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, L., et al. (2007). FT Protein movement contributes to long-distance signaling in floral induction in arabidopsis. Science 316, 1030-1036. doi: 10.1126/science.1141752
8. Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004). WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190. doi: 10.1101/gr.849004
9. Dubos, C., Stracke, R., Grotewold, E., Weisshaar, B., Martin, C., and Lepiniec, L. (2010). MYB transcription factors in Arabidopsis. Trends Plant Sci. 15, 573-581. doi: 10.1016/j.tplants.2010.06.005
10. Gilbertson, R. L., and Lucas, W. J. (1996). How do viruses traffic on the vascular higway? Trends Plant Sci. 1, 260-268. doi: 10.1016/1360-1385(96)10029-7
11. Gouy, M., Guindon, S., and Gascuel, O. (2010). SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221-224. doi: 10.1093/molbev/msp259
12. Hamel, L.-P., Nicole, M.-C., Sritubtim, S., Morency, M.-J., Ellis, M., Ehlting, J., et al. (2006). Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Trends Plant Sci. 11, 192-198. doi: 10.1016/j.tplants.2006.02.007
13. Harmer, S. L., Hogenesch, J. B., Straume, M., Chang, H. S., Han, B., Zhu, T., et al. (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290, 2110-2113. doi: 10.1126/science.290.5499.2110
14. Jaeger, K. E., Graf, A., and Wigge, P. A. (2006). The control of flowering in time and space. J. Exp. Bot. 57, 3415-3418. doi: 10.1093/jxb/erl159
15. Kardailsky, I., Shukla, V. K., Ahn, J. H., Dagenais, N., Christensen, S. K., Nguyen, J. T., et al. (1999). Activation tagging of the floral inducer FT. Science 286, 1962-1965. doi: 10.1126/science.286.5446.1962
16. Krusell, L., Madsen, L. H., Sato, S., Aubert, G., Genua, A., Szczyglowski, K., et al. (2002). Shoot control of root development and nodulation is mediated by a receptor-like kinase. Nature 420, 422-426. doi: 10.1038/nature01207
17. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948. doi: 10.1093/bioinformatics/btm404
18. Lata, C., and Prasad, M. (2011). Role of DREBs in regulation of abiotic stress responses in plants. J. Exp. Bot. 62, 4731-4748. doi: 10.1093/jxb/err210
19. Li, Y., Liu, Z. B., Shi, X., Hagen, G., and Guilfoyle, T. J. (1994). An auxin-inducible element in soybean SAUR promoters. Plant Physiol. 106, 37-43. doi: 10.1104/pp.106.1.37
20. Li, X., Wu, H. X., and Southerton, S. G. (2010). Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants. BMC Evol. Biol. 10:190. doi: 10.1186/1471-2148-10-190
21. Lin, M. K., Belanger, H., Lee, Y. J., Varkonyi-Gasic, E., Taoka, K., Miura, E., et al. (2007). FLOWERING LOCUS T protein may act as the long-distance florigenic signal in the cucurbits. Plant Cell 19, 1488-1506. doi: 10.1105/tpc.107.051920
22. Liu, H., Yu, X., Li, K., Klejnot, J., Yang, H., Lisiero, D., et al. (2008). Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science 322, 1535-1539. doi: 10.1126/science.1163927
23. Lough, T. J., and Lucas, W. J. (2006). Integrative plant biology: role of phloem long-distance macromolecular trafficking. Annu. Rev. Plant Biol. 57, 203-232. doi: 10.1146/annurev.arplant.56.032604.144145
24. Lucas, W. J., Groover, A., Lichtenberger, R., Furuta, K., Yadav, S. R., Helariutta, Y., et al. (2013). The Plant Vascular System: evolution, development and functions. J. Integr. Plant Biol. doi: 10.1111/jipb.12041
25. Lukowitz, W., Roeder, A., Parmenter, D., and Somerville, C. (2004). A MAPKK kinase gene regulates extra-embryonic cell fate in Arabidopsis. Cell 116, 109-119. doi: 10.1016/S0092-8674(03)01067-5
26. MAPK Group (Mitogen-activated protein kinases). (2002). Mitogen-activated protein kinase cascades in plants: a new nomenclature. Trends Plant Sci. 7, 301-308. doi: 10.1016/S1360-1385(02)02302-6
27. Meng, X., Wang, H., He, Y., Liu, Y., Walker, J., Torii, K., et al. (2012). A MAPK cascade downstream of ERECTA receptor-like protein kinase regulates Arabidopsis inflorescence architecture by promoting localized cell proliferation. Plant Cell 24, 4948-4960. doi: 10.1105/tpc.112.104695
28. Nei, M., and Kumar, S. (2000). Molecular Evolution and Phylogenetics. New York, NY: Oxford University Press.
29. Niklas, K. J. (1997). The Evolutionary Biology of Plants. Chicago, IL: University of Chicago Press.
30. Ottesen, E. A., Young, C. R., Eppley, J. M., Ryan, J. P., Chavez, F. P., Scholin, C. A., et al. (2013). Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc. Natl. Acad. Sci. U.S.A. 110, E488-E497. doi: 10.1073/pnas.1222099110
31. Pires, N., and Dolan, L. (2012). Morphological evolution in land plants: new designs with old genes. Phil. Trans. R. Soc. Lond. B Biol. Sci. 367, 508-518. doi: 10.1098/rstb.2011.0252
32. Prouse, M. B., and Campbell, M. M. (2012). The interaction between MYB proteins and their target DNA binding sites. Biochim. Biophys. Acta 1819, 67-77. doi: 10.1016/j.bbagrm.2011.10.010
33. Requena, A., Simón-Buela, L., Salcedo, G., and García-Arenal, F. (2006). Potential involvement of a cucumber of phloem protein 1 in the long distance movement of cucumber mosaic virus particles. Mol. Plant Microbe Interact. 19, 734-746. doi: 10.1094/MPMI-19-0734
34. Riaño-Pachón, D., Corrêa, L. G., Trejos-Espinosa, R. I., and Mueller-Roeber, B. (2008). Green transcription factors: a chlamydomonas overview. Genetics 179, 31-39.
35. Ruiz-Medrano, R., Guevara-González, R. G., Argüello-Astorga, G. R., Monsalve-Fonnegra, Z., Herrera-Estrella, L. R., and Rivera-Bustamante, R. F. (1999a). Identification of a sequence element involved in AC2-mediated transactivation of the pepper huasteco virus coat protein gene. Virology 253, 162-169. doi: 10.1006/viro.1998.9484
36. Ruiz-Medrano, R., Xoconostle-Cázares, B., and Lucas, W. J. (1999b). Phloem long-distance transport of CmNACP mRNA: implications for supracellular regulation in plants. Development 126, 4405-4419.
37. Ruiz-Medrano, R., Hinojosa-Moya, J. J., Xoconostle-Cázares, B., and Lucas, W. J. (2007). Influence of Cucumber mosaic virus infection on the mRNA population present in the phloem translocation stream of pumpkin plants. Funct. Plant Biol. 34, 292-301. doi: 10.1071/FP06300
38. Ruiz-Medrano, R., Xoconostle-Cázares, B., Ham, B.-K., Li, G., and Lucas, W. J. (2011). Vascular expression in Arabidopsis is predicted by the frequency of CT/GA-rich repeats in gene promoters. Plant J. 67, 130-144. doi: 10.1111/j.1365-313X.2011.04581.x
39. Santi, L., Wang, Y., Stile, M. R., Berendzen, K., Wanke, D., Roig, C., et al. (2003). The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox geneBKn3. Plant J. 34, 813-826. doi: 10.1046/j.1365-313X.2003.01767.x
40. Sauter, A., Davies, W. J., and Hartung, W. (2001). The long-distance abscisic acid signal in the droughted plant: the fate of the hormone on its way from root to shoot. J. Exp. Bot. 52, 1991-1199. doi: 10.1093/jexbot/52.363.1991
41. Schneidereit, A., Imlau, A., and Sauer, N. (2008). Conserved cis-regulatory elementsfor DNA-binding-with-one-finger and homeo-domain-leucine-zipper transcription factors regulate companion cell-specific expression of the Arabidopsis thaliana SUCROSE TRANSPORTER 2 gene. Planta 228, 651-662. doi: 10.1007/s00425-008-0767-4
42. Schwarz, R., and Dayhoff, M. (1979). "Matrices for detecting distant relationships, " in Atlas of Protein Sequences, ed M. Dayhoff (National Biomedical Research Foundation), 353-358.
43. Simón-Buela, L., and García-Arenal, F. (1999). Virus particles of cucumber green mottle mosaic tobamovirus move systemically in the phloem of infected cucumber plants. Mol. Plant Microbe Interact. 12, 112-118. doi: 10.1094/MPMI.1999.12.2.112
44. Sunter, G., and Bisaro, D. M. (1997). Regulation of a Geminivirus coat protein promoter by AL2 Protein (TrAP): evidence for activation and derepression mechanisms. Virology 232, 269-280. doi: 10.1006/viro.1997.8549
45. Tamaki, S., Matsuo, S., Wong, H. L., Yokoi, S., and Shimamoto, K. (2007). Hd3a protein is a mobile flowering signal in rice. Science 316, 1033-1036. doi: 10.1126/science.1141753
46. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739. doi: 10.1093/molbev/msr121
47. Taoka, K.-i., Ohki, I., Tsuji, H., Furuita, K., Hayashi, K., Yanase, T., et al. (2011). 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature 476, 332-335. doi: 10.1038/nature10272
48. Truernit, E., Bauby, H. L. N., Belcram, K., Barthélémy, J., and Palauqui, J.-C. (2012). OCTOPUS, a polarly localised membrane-associated protein, regulates phloem differentiation entry in Arabidopsis thaliana. Development 139, 1306-1315. doi: 10.1242/dev.072629
49. Xoconostle-Cázares, B., Xiang, Y., Ruiz-Medrano, R., Wang, H. L., Monzer, J., Yoo, B. C., et al. (1999). Plant paralog to viral movement protein that potentiates transport of mRNA into the phloem. Science 283, 94-98. doi: 10.1126/science.283.5398.94
50. Zwack, P. J., Shi, X., Robinson, B. R., Grupta, S., Compton, M. A., Gerken, D. M., et al. (2012). Vascular expression and C-terminal sequence divergence of cytokinin response factors in flowering plants. Plant Cell Physiol. 53, 1683-1695. doi: 10.1093/pcp/pcs110