Analysis of functional redundancies within the Arabidopsis TCP transcription factor family

Danisman S, van Dijk ADJ, Bimbo A, van der Wal F, Hennig L, de Folter S, Angenent GC, Immink RGH (2013)
Journal of Experimental Botany 64(18): 5673-5685.

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Abstract
Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein-protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein-protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family.
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Danisman S, van Dijk ADJ, Bimbo A, et al. Analysis of functional redundancies within the Arabidopsis TCP transcription factor family. Journal of Experimental Botany. 2013;64(18):5673-5685.
Danisman, S., van Dijk, A. D. J., Bimbo, A., van der Wal, F., Hennig, L., de Folter, S., Angenent, G. C., et al. (2013). Analysis of functional redundancies within the Arabidopsis TCP transcription factor family. Journal of Experimental Botany, 64(18), 5673-5685.
Danisman, S., van Dijk, A. D. J., Bimbo, A., van der Wal, F., Hennig, L., de Folter, S., Angenent, G. C., and Immink, R. G. H. (2013). Analysis of functional redundancies within the Arabidopsis TCP transcription factor family. Journal of Experimental Botany 64, 5673-5685.
Danisman, S., et al., 2013. Analysis of functional redundancies within the Arabidopsis TCP transcription factor family. Journal of Experimental Botany, 64(18), p 5673-5685.
S. Danisman, et al., “Analysis of functional redundancies within the Arabidopsis TCP transcription factor family”, Journal of Experimental Botany, vol. 64, 2013, pp. 5673-5685.
Danisman, S., van Dijk, A.D.J., Bimbo, A., van der Wal, F., Hennig, L., de Folter, S., Angenent, G.C., Immink, R.G.H.: Analysis of functional redundancies within the Arabidopsis TCP transcription factor family. Journal of Experimental Botany. 64, 5673-5685 (2013).
Danisman, Selahattin, van Dijk, Aalt D.J., Bimbo, Andrea, van der Wal, Froukje, Hennig, Lars, de Folter, Stefan, Angenent, Gerco C., and Immink, Richard G.H. “Analysis of functional redundancies within the Arabidopsis TCP transcription factor family”. Journal of Experimental Botany 64.18 (2013): 5673-5685.
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Su F, Shang D, Xu Y, Feng L, Yang H, Liu B, Su S, Chen L, Li X., Biomed Res Int 2015(), 2015
PMID: 26688819
TCP three-way handshake: linking developmental processes with plant immunity.
Lopez JA, Sun Y, Blair PB, Mukhtar MS., Trends Plant Sci. 20(4), 2015
PMID: 25655280
TCP14 and TCP15 mediate the promotion of seed germination by gibberellins in Arabidopsis thaliana.
Resentini F, Felipo-Benavent A, Colombo L, Blazquez MA, Alabadi D, Masiero S., Mol Plant 8(3), 2015
PMID: 25655823
Nitrate foraging by Arabidopsis roots is mediated by the transcription factor TCP20 through the systemic signaling pathway.
Guan P, Wang R, Nacry P, Breton G, Kay SA, Pruneda-Paz JL, Davani A, Crawford NM., Proc. Natl. Acad. Sci. U.S.A. 111(42), 2014
PMID: 25288754
Flower opening and closure: an update.
van Doorn WG, Kamdee C., J. Exp. Bot. 65(20), 2014
PMID: 25135521
Identification, cloning and characterization of the tomato TCP transcription factor family.
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The Arabidopsis immune adaptor SRFR1 interacts with TCP transcription factors that redundantly contribute to effector-triggered immunity.
Kim SH, Son GH, Bhattacharjee S, Kim HJ, Nam JC, Nguyen PD, Hong JC, Gassmann W., Plant J. 78(6), 2014
PMID: 24689742
Tetramer formation in Arabidopsis MADS domain proteins: analysis of a protein-protein interaction network.
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PMID: 24468197

43 References

Data provided by Europe PubMed Central.

miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis
Nag A, King S, Jack T., 2009
Control of leaf morphogenesis by microRNAs.
Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D., Nature 425(6955), 2003
PMID: 12931144
APE: Analyses of Phylogenetics and Evolution in R language.
Paradis E, Claude J, Strimmer K., Bioinformatics 20(2), 2004
PMID: 14734327
A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock.
Pruneda-Paz JL, Breton G, Para A, Kay SA., Science 323(5920), 2009
PMID: 19286557

AUTHOR UNKNOWN, 2010
AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.
Rehrauer H, Aquino C, Gruissem W, Henz SR, Hilson P, Laubinger S, Naouar N, Patrignani A, Rombauts S, Shu H, Van de Peer Y, Vuylsteke M, Weigel D, Zeller G, Hennig L., Plant Physiol. 152(2), 2010
PMID: 20032078
A gene expression map of Arabidopsis thaliana development
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU., 2005
Control of jasmonate biosynthesis and senescence by miR319 targets.
Schommer C, Palatnik JF, Aggarwal P, Chetelat A, Cubas P, Farmer EE, Nath U, Weigel D., PLoS Biol. 6(9), 2008
PMID: 18816164
class I TCPs modulate cytokinin-induced branching and meristematic activity in tomato
Steiner E, Yanai O, Efroni I, Ori N, Eshed Y, Weiss D., 2012
Evolution and diversification of the CYC/TB1 gene family in Asteraceae—a comparative study in Gerbera (Mutisieae) and sunflower (Heliantheae)
Tähtiharju S, Rijpkema AS, Vetterli A, Albert VA, Teeri TH, Elomaa P., 2012
RNA interference of the Arabidopsis putative transcription factor TCP16 gene results in abortion of early pollen development.
Takeda T, Amano K, Ohto MA, Nakamura K, Sato S, Kato T, Tabata S, Ueguchi C., Plant Mol. Biol. 61(1-2), 2006
PMID: 16786299
Thinking about genetic redundancy.
Thomas JH., Trends Genet. 9(11), 1993
PMID: 8310537
Multiple sequence alignment using ClustalW and ClustalX
Thompson JD, Gibson TJ, Higgins DG., 2002
A role for KNAT class II genes in root development
Truernit E, Haseloff J., 2007
A small-scale procedure for the rapid isolation of plant RNAs.
Verwoerd TC, Dekker BM, Hoekema A., Nucleic Acids Res. 17(6), 1989
PMID: 2468132
Gene expression map of the Arabidopsis shoot apical meristem stem cell niche
Yadav RK, Girke T, Pasala S, Xie M, Reddy GV., 2009

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