Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome

BMC Genomics
Claudia C EnglbrechtS Böhm

Abstract

The classical C2H2 zinc finger domain is involved in a wide range of functions and can bind to DNA, RNA and proteins. The comparison of zinc finger proteins in several eukaryotes has shown that there is a lot of lineage specific diversification and expansion. Although the number of characterized plant proteins that carry the classical C2H2 zinc finger motifs is growing, a systematic classification and analysis of a plant genome zinc finger gene set is lacking. We found through in silico analysis 176 zinc finger proteins in Arabidopsis thaliana that hence constitute the most abundant family of putative transcriptional regulators in this plant. Only a minority of 33 A. thaliana zinc finger proteins are conserved in other eukaryotes. In contrast, the majority of these proteins (81%) are plant specific. They are derived from extensive duplication events and form expanded families. We assigned the proteins to different subgroups and families and focused specifically on the two largest and evolutionarily youngest families (A1 and C1) that are suggested to be primarily involved in transcriptional regulation. The newly defined family A1 (24 members) comprises proteins with tandemly arranged zinc finger domains. Family C1 (64 members), ...Continue Reading

References

May 1, 1995·Plant Molecular Biology·B W Tague, H M Goodman
Jul 5, 1996·Biochemical and Biophysical Research Communications·H Takatsuji
Sep 20, 1996·The Journal of Biological Chemistry·H Takatsuji, T Matsumoto
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jan 6, 1999·Proceedings of the National Academy of Sciences of the United States of America·M LuoA M Chaudhury
Jan 27, 1999·Bioinformatics·S R Eddy
Apr 27, 2000·Trends in Biochemical Sciences·J Colasanti, V Sundaresan
Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·S A WolfeC O Pabo
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·M LuoA Chaudhury
Feb 28, 2001·Proceedings of the National Academy of Sciences of the United States of America·T XuL Bogorad
Mar 22, 2001·EMBO Reports·M CokolB Rost
Jul 17, 2001·The Journal of Biological Chemistry·K YoshiokaH Takatsuji
Mar 28, 2002·Nucleic Acids Research·Vivek AnantharamanL Aravind
Nov 13, 2002·Plant Physiology·José C ReyesWilhelm Gruissem
Mar 5, 2003·Chembiochem : a European Journal of Chemical Biology·Carla IserniaRoberto Fattorusso
Apr 16, 2003·The Plant Journal : for Cell and Molecular Biology·Keqiang WuBrian Miki
Oct 2, 2003·Genome Biology·Raul Urrutia
Nov 26, 2003·Journal of Molecular Biology·Javier Fernández-MartínezEduardo A Espeso
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Dec 19, 2003·Nucleic Acids Research·Ivica LetunicPeer Bork
Feb 20, 2004·Development·José R DinnenyDetlef Weigel
Aug 25, 2007·Genetics·Andrés Gaytán de Ayala AlonsoJürg Müller
Jan 1, 2002·The Arabidopsis Book·José Luis Riechmann

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Citations

Dec 15, 2011·Plant Cell Reports·Sravan Kumar JamiP B Kirti
Nov 22, 2007·Molecular Genetics and Genomics : MGG·Chang-Jie JiangHiroshi Takatsuji
Mar 19, 2011·Journal of Plant Research·Yasunari FujitaKazuko Yamaguchi-Shinozaki
Feb 20, 2010·Plant Molecular Biology·M Isabel OrdizRoger N Beachy
Jul 3, 2013·Journal of Proteome Research·Setsuko KomatsuPingfang Yang
Aug 30, 2008·Proceedings of the National Academy of Sciences of the United States of America·Changyin WuQifa Zhang
May 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jianghua ChenRujin Chen
Mar 4, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Delphine GourcilleauNathalie Leblanc-Fournier
Feb 22, 2012·Genome Biology and Evolution·M M PentonyM D Purugganan
Jan 12, 2011·Journal of Experimental Botany·Bernd Edlinger, Peter Schlögelhofer
Mar 27, 2009·Plant Physiology·Yoshiharu SawakiHiroyuki Koyama
Jun 12, 2013·Plant Physiology·Yoshinao OhyamaHiroyuki Koyama
Jun 23, 2006·PLoS Genetics·Frank WellmerElliot M Meyerowitz
Aug 24, 2012·PloS One·Santosh Kumar GuptaTilak R Sharma

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Methods Mentioned

BETA
histone acetylation
NMR
by
or

Software Mentioned

SAS
SMART
BLAST
Multiple Expectation Maximization for Motif Elicitation " ( ME...
ClustalX
PHYLIP
Pfam
HMMer
MEME

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