JnCML-like, an EF-hand motif-containing gene seasonally upregulated in the transition zone of black walnut (Juglans nigra L.)

Zhonglian Huang, Priyanka Surana, Daisuke Kihara, Richard Meilan, Keith Woeste

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DOI: 10.4236/ajmb.2011.13015                

Abstract

The economic value of a black walnut (Juglans nigra L.) tree is strongly determined by the quality and quantity of darkly colored heartwood in its stem. To understand the regulation of heartwood formation, we analyzed the region of heartwood formation in walnut stems (i.e., the transition zone, TZ) for the expression of 80 ESTs. Semi-quantitative RT-PCR and real-time PCR was performed to detect expression changes of candidate genes in the TZ and sapwood of trees harvested in summer and fall. Results revealed that the transcript of a clone containing two presumed EF-hand motifs was expressed at higher levels in the TZ than in other xylem tissues. Analysis of the full-length coding sequence revealed that the black walnut gene JnCML-like is similar to grancalcin-like calcium-binding EF hand proteins in Arabidopsis thaliana (At3g10300) and Zea mays (NM 001153810). A model of the predicted structure of JnCML-like showed it is similar to grancalcin and m-calpain, penta-EF-hand family proteins associated with cell proliferation, differentiation and programmed cell death. JnCML-like transcript was detected in tissue from the region of the pith meristem, and in roots, embryogenic callus, vascular cambium, female flowers, male flowers, green leaves, and partially and fully senescent leaves of black walnut, although transcript abundance varied considerably among these tissues.

Keywords

Transition Zone, M-Calpain, Juglans Nigra , Grancalcin

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Henikoff, S., Greene, E.A., Pietrokovski, S., Bork, P., Attwood, T.K. and Hood, L. (1997) Gene families: The taxonomy of protein paralogs and chimeras. Science, 278, 609-637. doi:10.1126/science.278.5338.609
[2]	Nakayama, S., Kawasaki, H. and Krestinger, R. (2000) Evolution of EF-hand proteins. In: Carafoli, E. and Krebs, J., Eds., Calcium Homeostasis, New York Springer.
[3]	Kretsinger, R.H. and Nockolds, C.E. (1973) Carp muscle calcium-binding protein II, Structure determination and general description. Journal of Biological Chemistry, 248, 3313-3326.
[4]	Day, I., Reddy, V.S., Ali, G.S. and Reddy, A.S.N. (2002) Analysis of EF-hand-containing proteins in Arabidopsis. Genome Biology, 3, 1-24. doi:10.1186/gb-2002-3-10-research0056
[5]	Nagata, T., Iizumi, S., Satoh, K., Ooka, H., Kawai, J., Carninci, P., Hayashizaki, Y., Otomo, Y., Murakami, K., Matsubara, K. and Kikuchi, S. (2004) Comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data. Molecular Biology and Evolution, 21, 1855-1870. doi:10.1093/molbev/msh197
[6]	Maki, M., Kitaura, Y., Satoh, H., Ohkouchi, S. and Shibata, H. (2002) Structures, functions and molecular evolution of the penta-EF-hand Ca2+ binding proteins. Biochim Biophysica Acta, 1600, 51-60.
[7]	Johnson, K.L., Faulkner, C., Jeffree, C.E. and Ingram, G.C. (2008) The phytocalpain Defective Kernel 1 is a novel arabidopsis growth regulator whose activity is regulated by proteolytic processing. Plant Cell, 20, 2619-2630. doi:10.1105/tpc.108.059964
[8]	Spicer, R. (2005) Senescence in secondary xylem: Heartwood formation as an active developmental program. In: Holbrook, N.M. and Zwieniecki, M.A., Eds., Vascular Transport in Plants, Elsevier Academic Press, Amsterdam, 457-475. doi:10.1016/B978-012088457-5/50024-1
[9]	Andrews, J.A. and Siccama, T.G. (1999) Restranslocation of calcium and magnesium at the heartwood sapwood boundary of Atlantic white cedar. Ecology, 76, 659-663. doi:10.2307/1941225
[10]	Berthier, S., Kokutse, A.D., Stokes, A. and Fourcaud, T. (2001) Irregular heartwood formation in Maritime pine (Pinus pinaster Ait.): Consequences for biomechanical and hydraulic tree functioning. Annals of Botany, 87, 19-25. doi:10.1006/anbo.2000.1290
[11]	Dehon, L., Macheix, J.J. and Durand, M. (2002) In-volvement of peroxidases in the formation of the brown coloration of heartwood in Juglans nigra. Journal of Ex-perimental Botany, 53, 303-311. doi:10.1093/jexbot/53.367.303
[12]	Yang, J., Kamdem, D.P., Keathley, D.E. and Han, K.H. (2004) Seasonal changes in gene expression at the sapwood-heartwood transition zone of black locust (Robinia pseudoacacia) revealed by cDNA microarray analysis. Tree Physiology, 24, 461-474.
[13]	Spicer, R. and Holbrook, N.M. (2007) Parenchyma cell respiration and survival in secondary xylem: Does metabolic activity decline with age? Plant and Cell Environment, 30, 934-943. doi:10.1111/j.1365-3040.2007.01677.x
[14]	Nakaba, S., Kubo, T. and Funada, R. (2008) Differences in patterns of cell death between ray parenchyma cells and ray tracheids in the conifers Pinus densiflora and Pinus rigida. Trees, 22, 623-630. doi:10.1007/s00468-008-0220-0
[15]	Hillis, W.E. (1987) Heartwood and tree exudates. Springer-Verlag, Berlin, New York.
[16]	Nelson, N.D. (1978) Xylem ethylene, phenol-oxidizing enzymes and nitrogen and heartwood formation in walnut and cherry. Canadian Journal of Botany, 56, 626-634. doi:10.1139/b78-070
[17]	Frey-Wyssling, A. and Bosshard, H.H. (1959) Cytology of the ray cells in sapwood and heartwood. Holzforschung, 13, 129-137. doi:10.1515/hfsg.1959.13.5.129
[18]	Bosshard, H.H. (1965) Aspects of the ageing process in cambium and xylem. Holzforschung, 19, 65-69. doi:10.1515/hfsg.1965.19.3.65
[19]	Hauch, S. and Magel, E. (1998) Extractable activities and protein content of sucrose phosphate synthase, sucrose synthase and neutral invertase in trunk tissues of Robinia pseudoacacia L. are related to cambial wood production and heartwood formation. Planta, 207, 266-274. doi:10.1007/s004250050482
[20]	Chapple, C.S., Vogt, T., Ellisyba, B.E. and Somerville, C.R. (1992) An Arabidopsis mutant defective in the general phenylpropanoid pathway. Plant Cell, 4, 1413-1424.
[21]	Kolosova, N., Miller, B., Ralph, S., Ellis, B.E., Douglas, C., Ritland, K. and Bohlmann, J. (2004) Isolation of high-quality RNA from gymnosperm and angiosperm trees. Biotechnology, 36, 821-824.
[22]	Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406-3415. doi:10.1093/nar/gkg595
[23]	Huang, Z., Tsai, C.J., Harding, S., Meilan, R. and Woeste, K.E. (2009) A Cross-species transcriptional profile analysis of heartwood formation in black walnut. Plant Molecular Biology Reporter, 28, 222-230. doi:10.1007/s11105-009-0144-x
[24]	Kim, B-R., Nam, H-Y., Kim, S-I. and Chang, Y. J. (2004) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotech Letters, 25, 1869-1872. doi:10.1023/A:1026298032009
[25]	Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. doi:10.1093/bioinformatics/btm404
[26]	Papadopoulos, J.S. and Agarwala, R. (2007) COBALT: Constraint-based alignment tool for multiple protein sequences. Bioinformatics, 23, 1073-1079. doi:10.1093/bioinformatics/btm076
[27]	Liu, S., Zhang, C., Liang, S. and Zhou, Y. (2007) Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins, 68, 636-645. doi:10.1002/prot.21459
[28]	Eswar, N., Eramian, D., Webb, B., Shen, M.Y. and Sali, A. (2008) Protein structure modeling with MODELLER. Methods in Molecular Biology, 426,145-159. doi:10.1007/978-1-60327-058-8_8
[29]	Jackson, D., Veit, B. and Hake, S. (1994) Expression of maize KNOTTED1 related homeobox genes in the shoot apical meristem predicts patterns of morphogenesis in the vegetative shoot. Development, 120, 405-413.
[30]	Schwacke, R., Schneider, A., Van Der Graaff, E., Fischer, K., Catoni, E., Desimone, M., Frommer, W.B., Flugge, U.I. and Kunze, R. (2003) ARAMEMNON, a novel database for arabidopsis integral membrane proteins. Plant Physiology, 131, 16-26. doi:10.1104/pp.011577
[31]	Xu, P., Roes, J., Segal, A.W. and Radulovic, M. (2006) The role of grancalcin in adhesion of neutrophils. Cellular Immunology, 240, 116-121. doi:10.1016/j.cellimm.2006.07.004
[32]	Shao, H., Chou, J., Baty, C.J., Burke, N.A., Watkins, S.C., Stolz, D.B. and Wells, A. (2006) Spatial localization of m-Calpain to the plasma membrane by phosphoinositide bisphosphate binding during epidermal growth factor receptor-mediated activation. Molecular Cell Biology, 26, 5481-5496. doi:10.1128/MCB.02243-05
[33]	Hosfield, C.M., Elce, J.S., Davies, P.L. and Jia, Z. (1999) Crytal structure of calpain reveals the structural basis for Ca (2+)-dependent protease activity and a novel mode of enzyme activation. EMBO Journal, 18, 6880-6889. doi:10.1093/emboj/18.24.6880
[34]	Orrenius, S., Zhivotovsky, B. and Nicotera, P. (2003) Regulation of cell death: The calcium apoptosis link. Nature Reviews Molecular Cell Biology, 4, 552-565. doi:10.1038/nrm1150
[35]	Lautner, S. and Fromm, J. (2009) Calcium-dependent physiological processes in trees. Plant Biology, 12, 268-274. doi:10.1111/j.1438-8677.2009.00281.x
[36]	Hillinger, C., Holl, W. and Ziegler, H. (1996) Lipids and lipolytic enzymes in the trunkwood of Robinia pseudoacacia L. during heartwood formation. Tree, 10, 376-381.
[37]	Newell, E. A., Mulkey, S.S. and Wright, S.J. (2002) Seasonal patterns of carbohydrate storage in four tropical tree species. Oecologia, 131, 333-342. doi:10.1007/s00442-002-0888-6
[38]	Magel, E. (2000) Biochemistry and physiology of heart-wood formation. In: Savidge, R., Barnett, J. and Napier, R., Eds., Molecular and Cell Biology of Wood Formation. BIOS Scientific Publishers, Oxford.
[39]	van Doorn, W.G. and Woltering, E.J. (2005) Many ways to exit? Cell death categories in plants. Trends in Plant Science, 10, 117-122. doi:10.1016/j.tplants.2005.01.006
[40]	Lim, P.O., Kim, H.J. and Nam, H.G. (2007) Leaf senes-cence. Annual Review Plant Physiology, 58, 115-136.