Phylogenetic Study of Plant Q-type C2H2 Zinc Finger Proteins and Expression Analysis of Poplar Genes in Response to Osmotic, Cold and Mechanical Stresses

DNA RESEARCH 18, 77–92, (2011) Advance Access Publication: 2 March 2011 doi:10.1093/dnares/dsr001 Phylogenetic Study of Plant Q-type C2H2 Zinc Finger Proteins and Expression Analysis of Poplar Genes in Response to Osmotic, Cold and Mechanical Stresses DELPHINE Gourcilleau 1,†, CATHERINE Lenne 1,*, †, CLAUDIA Armenise 1, BRUNO Moulia 2, JEAN-LOUIS Julien 1, GISÈLE Bronner 3, *, and NATHALIE Leblanc-Fournier 1,* Clermont Université, Université Blaise Pascal, UMR 547 Physique et Physiologie Intégratives de l’Arbre Fruitier et Forestier, 24 avenue des Landais, BP 10448, 63177 Aubière Cedex, France1; INRA, UMR 547 Physique et Physiologie Intégratives de l’Arbre Fruitier et Forestier, 234 avenue du Brézet, 63100 Clermont-Ferrand, France2 and Clermont Université, Université Blaise Pascal, UMR Laboratoire des Microorganismes: Génome et Environnement, 24 avenue des Landais, 63177 Aubière Cedex, France3 *To whom correspondence should be addressed. Tel. þ33 4 73 40 79 26 (C.L.), þ33 4 73 40 78 37 (G.B.), þ33 4 73 30 79 30 (N.L.-F.). Fax. þ33 4 73 40 79 16 (C.L.), þ33 4 73 40 76 70 (G.B.), þ33 4 73 40 79 16 (N.L.-F.). Email: (C.L.), (G.B.), nathalie. (N.L.-F.) Edited by Satoshi Tabata (Received 28 September 2010; accepted 20 January 2011) Abstract Plant Q-type C2H2 zinc finger transcription factors play an important role in plant tolerance to various environmental stresses such as drought, cold, osmotic stress, wounding and mechanical loading. To carry out an improved analysis of the specific role of each member of this subfamily in response to mechanical loading in poplar, we identified 16 two-fingered Q-type C2H2-predicted proteins from the poplar Phytozome database and compared their phylogenetic relationships with 152 two-fingered Q-type C2H2 protein sequences belonging to more than 50 species isolated from the NR protein database of NCBI. Phylogenetic analyses of these Q-type C2H2 proteins sequences classified them into two groups G1 and G2, and conserved motif distributions of interest were established. These two groups differed essentially in their signatures at the C-terminus of their two QALGGH DNA-binding domains. Two additional conserved motifs, MALEAL and LVDCHY, were found only in sequences from Group G1 or from Group G2, respectively. Functional significance of these phylogenetic divergences was assessed by studying transcript accumulation of six poplar C2H2 Q-type genes in responses to abiotic stresses; but no group specificity was found in any organ. Further expression analyses focused on PtaZFP1 and PtaZFP2, the two genes strongly induced by mechanical loading in poplars. The results revealed that these two genes were regulated by several signalling molecules including hydrogen peroxide and the phytohormone jasmonate. Key words: C2H2; phylogenetic analysis; abiotic stress; mechanical loading 1. Introduction Transcription factors play a key role in modulating the acclimation response of plants to various internal † These authors contributed equally to this article. or external cues. A subset of these transcription factors belongs to the zinc finger proteins (ZFPs) characterized by zinc finger domains (ZFs) enabling protein interaction with DNA. The term “zinc finger” refers to a protein motif that binds a zinc ion in order to stabilize its three-dimensional structure consisting of a two-stranded antiparallel b-sheet and # The Author 2011. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 78 Q-type C2H2 Zinc Finger Proteins a-helix.1 ZFPs are classified according to the number and the order of the Cys (cysteine) and His (histidine) residues that bind the zinc ion. Among these different ZFPs types, C2H2-ZFPs are one of the most abundant and often studied transcription factors in eukaryotes.2 In silico analysis has shown that 3% of all genes in mammals, 2.3% in Diptera, 0.8% in Saccharomyces cerevisiae and 0.7% in Arabidopsis thaliana encode C2H2-ZFPs.3 In A. thaliana, more than 2000 potential transcription factors have been identified,4,5 of which 9% belong to the C2H2-ZFP family. C2H2-ZFPs are characterized by a conserved sequence CX2 – 4CX3FX5LX2HX3-5H (where underlined C and H represent Cys and His interacting with the zinc ion). Plant C2H2-ZFPs possess one to five ZFs. Two main features distinguish most of them from other eukaryote C2H2-ZFPs. First, most plant C2H2ZFPs contain an invariant QALGGH motif inside the ZF, whereas yeast and animals do not. Second, for multiple-fingered C2H2-ZFPs, ZFs are separated by longer spacers than in other eukaryotes.1,6 Both the QALGGH motif and length of sequences between two successive ZFs are thought to be important for the affinity of the protein to its DNA target.6 – 8 C2H2-ZFPs can be divided into three classes according to the number, types and arrangement of ZFs.3,9 According to an in silico genome-wide comparative analysis performed in A. thaliana,3 two classes, A and B, encompass ZFPs that contain tandem ZFs in one or in more than one array, respectively (as proposed earlier for yeast genome). Class C corresponds to ZFPs containing a single ZF or dispersed ZFs (ZFs being considered dispersed when more than 10 amino acid (AA) residues separate two consecutive ZFs). Most C2H2-ZFPs in animals and yeast can be classified in Classes A and B, but plant C2H2-ZFPs are found mainly in Class C. This third class can be divided into three subclasses according to the number of AA residues separating the two invariant His of the ZFs: three, four or five residues for Subclasses C1, C2 and C3, respectively. Inside Subclass C1, 85% of the C2H2 proteins contain strictly the QALGGH motif (or with few modifications),3 also called Q-type ZFs in rice.3,10 In silico studies on ZFPs have identified 64 Q-type C2H2ZFPs in A. thaliana,3 99 in rice (Oryza sativa)10 and 47 in bread wheat (Triticum aestivum).11 First considered exclusively as transcription factors with sequence-specific binding to DNA, ZFPs are now known to recognize RNA or other proteins.12 However, their role as transcription factors is still most often studied. In plants, the C2H2 proteins belonging to Class C are the largest family. They are involved in a wide range of processes including development and organogenesis along with response to stress and defence pathways. These proteins have [Vol. 18 been shown to be involved in salt stress, cold, dehydration and light stress in A. thaliana,13 – 16 the switch from vegetative to floral development and drought in rice,11,17 flower development and drought in Petunia,18,19 pathogen defence in Capsicum annuum 20 and water and salt stress in Thellungiella halophila (...truncated)