106 Opinion TRENDS in Plant Science Vol.7 No.3 March 2002 We gave a generic name (AtbZIP1–AtbZIP75) to bZIP transcription each bZIP gene (Fig. 1), including those that had been named (sometimes twice) before. Our numbering system does not follow a distinct rationale factors in Arabidopsis but provides a unique identifier for each bZIP gene, as proposed for R2R3-MYB and WRKY TFs [2,3] and should help communication in the scientific The bZIP Research Group (Marc Jakoby et al.) community. Our results and the structured nomenclature were incorporated into the MAtDB database at MIPS (Munich Information Center for In plants, basic region/leucine zipper motif (bZIP) transcription factors Protein Sequences). regulate processes including pathogen defence, light and stress signalling, seed maturation and flower development. The Arabidopsis genome sequence Complexity of the bZIP family in Arabidopsis contains 75 distinct members of the bZIP family, of which ~50 are not Putative AtbZIP proteins were clustered according described in the literature. Using common domains, the AtbZIP family can be to sequence similarities of their basic region. subdivided into ten groups. Here, we review the available data on bZIP Subsequently, the MEME analysis tool functions in the context of subgroup membership and discuss the interacting (http://meme.sdsc.edu/meme/website/meme.html) proteins. This integration is essential for a complete functional characterization was used to search for domains shared by the AtbZIP of bZIP transcription factors in plants, and to identify functional redundancies proteins. This allowed us to define ten groups of bZIPs among AtbZIP factors. with a similar basic region and additional conserved motifs (Fig. 1). Proteins from the same groups also Transcription factors (TFs) play crucial roles in have additional features in common, such as the size almost all biological processes. Structurally, TFs are of the leucine zipper (Table 1). Three AtbZIP proteins usually classified by their DNA-binding domains: that did not fit into any group were not classified. basic region/leucine zipper (bZIP) TFs have a basic Our classification is not based purely on phylogeny region that binds DNA and a leucine zipper and is, therefore, partly subjective. Because we put dimerization motif (Box 1). Proteins with bZIP some emphasis on conserved motifs, we hope that it domains are present in all eukaryotes analysed to reflects functional similarities and should aid in date. Some, such as Jun/Fos or CREB, have been determining specific functions for each bZIP. studied extensively in animals and serve as models for understanding TF–DNA interactions, ternary Structural features and functional characterization complex formation and TF post-translational For each of the ten bZIP groups, we review the modifications (Box 1). structural features and functional information Arabidopsis has about four times as many bZIP available from Arabidopsis and other plant species. Marc Jakoby genes as yeast, worm and human [1]. Genetic and The bZIPs from other plants were aligned with Bernd Weisshaar MPI for Plant Breeding molecular studies of a few of these Arabidopsis AtbZIPs to determine which group they matched Research, 50829 Köln, thaliana bZIP (AtbZIP) factors show that they with. Because members of a given group share a Germany. regulate diverse biological processes such as similar DNA-binding basic region, many of them Wolfgang Dröge-Laser pathogen defence, light and stress signalling, seed probably recognize similar cis elements. However, Albrecht-von-Haller- maturation and flower development. The early the limited number of binding site selection Institut, Untere Karspüle recruitment of bZIP TFs in plant evolution might experiments performed to date does not allow us to 2, D-37073 Göttingen, Germany. contribute to this diversity, which contrasts with confirm this hypothesis (Table 1). the apparently more confined functions of the Jesus Vicente-Carbajosa Dept Biotecnologia, plant-specific R2R3-MYB and WRKY TFs [2,3]. Group A ETSIA Universidad As a basis for future functional analysis, we Seven members of group A have been studied Politecnica, 28040 Madrid, present an overview of the potential AtbZIP genes (AtbZIP39/ABI5, AtbZIP36/ABF2/AREB1, Spain. encoded in the Arabidopsis genome. Using optimized AtbZIP38/ABF4/AREB2, AtbZIP66/AREB3, Jens Tiedemann gene predictions based on known bZIP gene AtbZIP40/GBF4, AtbZIP35/ABF1 and Institut für structure and cDNA sequences obtained in our AtbZIP37/ABF3) and most of the functional Pflanzengenetik und Kulturpflanzenforschung laboratories via the REGIA (Regulatory Gene information available suggests roles in abscisic acid (IPK), Corrensstrasse 3, Initiative in Arabidopsis) European project, we (ABA) or stress signalling [4–7]. In vegetative 06466 Gatersleben, identified 75 putative genes encoding proteins with tissues, ABA and abiotic stresses such as cold, Germany. the bZIP signature (Box 1). Genes that were drought or high salinity induce gene expression Thomas Kroj annotated as ‘bZIP’ in the various databases through cis elements that include the ABA response François Parcy* (TAIR, MAtDB, EMBL/GenBank, TIGR) but that do element (ABRE). ABRE binding factor (ABF) and Institut des Sciences du Végétal, CNRS, not show the exact bZIP signature were excluded ABA-responsive element binding protein (AREB) 1 avenue de la terrasse, from our analysis. Because our total number differs proteins can bind to different ABRE-containing 91190 Gif-sur-Yvette, from the 81 bZIP genes identified by Jose Luis promoters in vitro or in yeast [4,7]. The available France. *e-mail: Riechmann et al. [1], we cannot exclude the existence data indicate that ABA or abiotic stresses induce [email protected] of a few additional AtbZIP genes. ABF/AREB expression and that ABA triggers http://plants.trends.com 1360-1385/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved. PII: S1360-1385(01)02223-3 Opinion TRENDS in Plant Science Vol.7 No.3 March 2002 107 Box 1. What is a bZIP protein? The bZIP domain consists of two structural interaction surface of the helices [a]. d Fukazawa, J. et al. (2000) REPRESSION OF features located on a contiguous α-helix Examples of known heterodimerizations in SHOOT GROWTH, a bZIP transcriptional (Fig. I) [a]: first, a basic region of ~16 amino plants are listed in Table 1 in the main text. activator, regulates cell elongation by controlling the level of gibberellins. acid residues containing a nuclear Plant bZIP proteins preferentially bind Plant Cell 12, 901–915 localization signal followed by an invariant to DNA sequences with an ACGT core. N-x7-R/K motif that contacts the DNA; and, Binding specificity is regulated by second, a heptad repeat of leucines or other flanking nucleotides. Plant bZIPs bulky hydrophobic amino acids positioned preferentially bind to the A-box (TACGTA), exactly nine amino acids towards the C-box (GACGTC) and G-box (CACGTG) C-terminus, creating an amphipathic helix. [b], but there are also examples of To bind DNA, two subunits adhere via nonpalindromic binding sites [c,d]. interactions between the hydrophobic References sides of their helices, which creates a a Hurst, H.C. (1995) Transcription factors 1: superimposing coiled-coil structure (the bZIP proteins. Protein Profile 2, 101–168 so-called zipper; Fig. II). The ability to form b Izawa, T. et al. (1993) Plant bZIP protein DNA binding specificity. J. Mol. Biol. 230, 1131–1144 homo- and heterodimers is influenced by c Choi, H. et al. (2000) ABFs, a family of ABA- the electrostatic attraction and repulsion of responsive element binding factors. J. Biol. polar residues flanking the hydrophobic Chem. 275, 1723–1730 Basic region Leucine zipper N –– x7 R/K –x9 –L ––––x6 L x6 L TRENDS in Plant Science Fig. II. Three-dimensional structure of the GCN4 Fig. I. Primary structure of the bZIP domain. The basic region is shaded in blue and the highly conserved bZIP domain bound to DNA. The leucine residues residues are highlighted with blue and red boxes. A consensus sequence is given below. The leucines are are positioned on one side of each helix and form sometimes replaced by isoleucine, valine, phenylalanine or methionine. coiled coils via van der Waals interactions. AREB1/2 phosphorylation. This phosphorylation is crispum) CPFR2 (Table 1). Most remarkable in this necessary for AREB1/2 to induce downstream genes group, is an extended leucine zipper with up to nine and could occur on the casein kinase II (CKII) heptad repeats. In addition, potential target sites for phosphorylation sites present in the conserved protein modification such as phosphorylation sites domains (Fig. 1). ABA and stress therefore probably that regulate nuclear translocation and DNA-binding induce both transcriptional and post-translational properties are also conserved [10]. The information regulation of several group-A bZIPs. available on Opaque2 and closely related monocot During late seed development, ABA induces the genes indicates that they regulate seed storage expression of the late embryogenesis abundant (LEA) protein production by interacting with the PBF genes, which are thought to participate in the protein [11–14], whereas CPFR2 and G/HBF-1 acquisition of desiccation tolerance. Later, ABA also might be involved in responses to environmental or blocks seed germination and early seedling pathogen challenge [15,16]. It will be interesting to development. Analysis of the abi5 mutant phenotype test whether the closest Opaque2 homologues shows