bZIP Proteins Research Articles

Analysis of the spacing between the two palindromes of activation sequence-1 with respect to binding to different TGA factors and transcriptional activation potential.

In higher plants, activation sequence-1 (as-1) of the cauliflower mosaic virus 35S promoter mediates both salicylic acid- and auxin-inducible transcriptional activation. Originally found in viral and T-DNA promoters, as-1-like elements are also functional elements of plant promoters activated in the course of a defence response upon pathogen attack. as-1-like elements are characterised by two imperfect palindromes with the palindromic centres being spaced by 12 bp. They are recognised by plant nuclear as-1-binding factor ASF-1, the major component of which is basic/leucine zipper (bZIP) protein TGA2.2 (approximately 80%) in Nicotiana tabacum. In electrophoretic mobility shift assays, ASF-1 as well as bZIP proteins TGA2.2, TGA2.1 and TGA1a showed a 3-10-fold reduced binding affinity to mutant as-1 elements encoding insertions of 2, 4, 6, 8 or 10 bp between the palindromes, respectively. This correlated with a 5-10-fold reduction in transcriptional activation from these elements in transient expression assays. Although ASF-1 and TGA factors bound efficiently to a mutant element carrying a 2 bp deletion between the palindromes [as-1/(-2)], the latter was strongly compromised with respect to mediating gene expression in vivo. A fusion protein consisting of TGA2.2 and a constitutive activation domain mediated transactivation from as-1/(-2) demonstrating binding of TGA factors in vivo. We therefore conclude that both DNA binding and transactivation require optimal positioning of TGA factors on the as-1 element.

The possible involvement of a phosphate-induced transcription factor encoded by phi-2 gene from tobacco in ABA-signaling pathways.

A novel phosphate-induced gene, phi-2, has been identified by its induction on addition of phosphate to phosphate-starved tobacco BY-2 cells. The predicted gene product of phi-2 has significant homology to a group of bZIP proteins involved in ABA-signaling pathways, and phi-2 also responded to ABA treatment. A previously isolated phosphate-induced gene, phi-1, (Sano et al. (1999) Plant Cell Physiol. 40: 1) was also responsive to ABA. Although phosphate addition induced semi-synchronous cell division in phosphate-starved tobacco BY-2 cells, ABA adversely affected cell division. Detailed examination revealed that the high levels of phosphate required to induce semi-synchronous cell division seemed to be perceived as indicators of stress by the cells. One of the stress indicators perceived by the cells is a cytoplasmic pH change, to which phi-2 and phi-1 genes respond. The different components of the cell's response to phosphate induction are discussed.

The detection of the meq gene in chicken infected with Marek's disease virus serotype 1.

In the genome of strains of very virulent Marek's disease virus serotype 1(vvMDV1), such as Md5 and RB1B, the meq open reading frame (ORF) encoding a 339-amino-acid bZIP protein, is present, while a slightly longer meq ORF, termed as L-meq, in which a 180-bp sequence is inserted into the meq ORF is found in other strains of MDV1, such as CV1988/R6 and attenuated JM. When chickens were infected with vvMDV1 strains and the meq gene was amplified by nested polymerase chain reaction (PCR), the meq gene was detected throughout the experimental period for 7 weeks post inoculation (pi). However, the L-meq gene was also detected at 3 to 5 weeks and 3 to 4 weeks pi. in Md5-infected and RB1B-infected chickens, respectively. In the case of chickens infected with an attenuated MDV1, the JM strain, the L-meq gene was detected at 2 to 7 weeks pi., and the meq gene was also detected at 2 to 6 weeks pi. Both L-meq and meq genes were detected in chickens infected with an attenuated nononcogenic vaccine strain of MDV1 (CVI988/R6), throughout the experimental period. Though quantitative PCR was not performed, a larger amount of the PCR products corresponding to the L-meq than the meq gene was amplified from chickens infected with JM or CVI988/R6. These results suggest that a dynamic population shift between the MDV subpopulations displaying meq and L-meq genes occurs in chickens during the course of MDV infection. Since the MDV subpopulation that displays the L-meq gene only displays it during the latent phase, the L-meq and its gene product, if any, might contribute to the maintenance of the MDV latency.

Interaction of rice bZIP protein REB with the 5?- upstream re-gion of both rice sbe1 gene and waxy gene

Rice starch branching enzyme 1 (SBE1) and granule-bound starch synthase (GBSS) catalyzed the biosynthesis of amylopectin and amylose in rice developing endosperm respectively, and the genes encoding these two enzymes, sbe1 and waxy, are mainly expressed in the endosperm. Within the 5′-upstream region of rice sbe1 gene, we identified a 53 bp fragment C53 which could interact with the nuclear proteins extracted from rice endosperm. We also found that fragment Ha-2 in the 5′-upstream region of rice waxy gene could compete with C53 for its interaction. Further experiments demonstrated that rice bZIP protein REB could interact with two ACGT elements (G-box and Hex) in the fragment C53 as well as three ACGT elements (WG1, WG2, and WG3) in the fragment Ha-2. The WG1 element could compete well with Hex element for its interaction with REB. These results suggested that the expression of sbe1 and waxy gene in rice developing endosperm may be coordinately regulated by REB-like bZIP transcriptional factors.

Rice bZIP protein, REB, interacts with GCN4 motif in promoter of Waxy gene

A bifactorial endosperm box (EB), which contains an endosperm motif (EM) and a GCN4 motif, was found in rice Wx promoter. EB was found in 5' upstream region of many seed storage protein genes accounting for these genes expression exclusive in endosperm among various cereals. Many reports demonstrated that the bZIP transcription activators isolated from wheat, barley and maize, etc. regulate the gene expression through binding to the GCN4 motif. In this research, we showed that GCN4 sequence could be recognized by nuclear proteins extracted from immature rice seeds. Furthermore, a rice bZIP protein, REB was isolated by using PCR method and REB fusion protein was expressed in E. coli. The results of gel shift analysis showed that REB could recognize and bind to the GCN4 motif in the Wx gene in addition to binding to the target sequence in the promoter of alpha-globulin.

Design and Synthesis of a Peptide That Binds Specific DNA Sequences through Simultaneous Interaction in the Major and in the Minor Groove This work was supported by the Spanish M.E.C. (PB97-0524) and the Xunta de Galicia (PGIDT00PXI20912PR). M.E.V. and A.M.C. thank the Xunta de Galicia and the University of Santiago for their predoctoral fellowships. We are very grateful to Prof.

A bivalent system capable of binding to hybrid DNA sites through simultaneous interaction in the major and the minor groove (see schematic representation) is formed by appropriate linking of the basic region of a b-ZIP protein (GCN4) to a tripyrrole related to the antibiotic distamycin.

Phylogenetic relationships between Arabidopsis and sugarcane bZIP transcriptional regulatory factors

We built a complete and non-redundant database of bZIP transcriptional regulatory factors from the Arabidopsis reference genome. These Arabidopsis bZIP factors were ordered into thirteen families of evolutionary related proteins and this classification was used to identify and organize sugarcane cDNAs encoding bZIP proteins. We also show how this classification should help in defining putative clusters of orthologous groups of higher plant bZIP regulators and briefly discuss the expected benefits of this procedure to efficiently characterize sugarcane bZIP transcriptional regulators.

Regulation of cyclic peptide biosynthesis in a plant pathogenic fungus by a novel transcription factor.

Strains of the filamentous fungus Cochliobolus carbonum that produce the host-selective compound HC-toxin, a cyclic tetrapeptide, are highly virulent on certain genotypes of maize (Zea mays L.). Production of HC-toxin is under the control of a complex locus, TOX2, which is composed of at least seven linked and duplicated genes that are present only in toxin-producing strains of C. carbonum. One of these genes, TOXE, was earlier shown to be required for the expression of the other TOX2 genes. TOXE has four ankyrin repeats and a basic region similar to those found in basic leucine zipper (bZIP) proteins, but lacks any apparent leucine zipper. Here we show that TOXE is a DNA-binding protein that recognizes a ten-base motif (the "tox-box") without dyad symmetry that is present in the promoters of all of the known TOX2 genes. Both the basic region and the ankyrin repeats are involved in DNA binding. A region of TOXE that includes the first ankyrin repeat is necessary and sufficient for transcriptional activation in yeast. The data indicate that TOXE is the prototype of a new family of transcription factor, so far found only in plant-pathogenic fungi. TOXE plays a specific regulatory role in HC-toxin production and, therefore, pathogenicity by C. carbonum.

A GCN4 variant with a C-terminal basic region binds to DNA with wild-type affinity.

Basic-region leucine zipper (bZip) proteins contain a bipartite DNA-binding motif consisting of a leucine zipper dimerization domain and a basic region that directly contacts DNA. In all naturally occurring bZip proteins, the basic region is positioned N-terminal to the leucine zipper. We have designed a series of model bZip peptides in which the basic region of the yeast transcriptional activator GCN4 is placed C-terminal to its leucine zipper. DNA-binding studies demonstrate that the optimal reverse GCN4 (rGCN4) peptide is able to bind specifically and with wild-type affinity to DNA despite this unnatural arrangement of the two subdomains. These results suggest that a thermodynamic basis for the observed N-terminal positioning of the basic region relative to the dimerization domain is unlikely.

The role of E2A-PBX1 in leukemogenesis.

A signi®cant number of the malignancies of the immune system are the result of nonrandom chromosomal translocations that cause either the overexpression of endogenous genes or the production of novel chimeric factors that can promote uncontrolled cell growth and block di€erentiation. Translocations which fuse the gene encoding the basic helix ± loop ± helix transcription factor E2A with either the gene encoding the homeodomain protein PBX1 or the bZIP protein HLF result in the generation of chimeric proteins that can cause preand pro-B cell acute lymphoblastic leukemias (ALL), respectively. What is currently known about the E2A-HLF fusion protein is reviewed elsewhere in this issue. This review focuses on the mechanisms and models of E2A-PBX1-mediated pre-B cell transformation.

Trans-dominant suppression of plant TGA factors reveals their negative and positive roles in plant defense responses.

Salicylic acid (SA) is a key regulator for the induction of systemic acquired resistance (SAR), and NPR1 is a critical mediator for the biological effects of SA. Physical interactions between NPR1 and TGA factors, a conserved family of basic-leucine-zipper (bZip) proteins in plants, have suggested a role for these transcription factors in mediating SAR induction via the regulation of defense genes. To elucidate this function, we constructed a trans-dominant mutant that specifically eliminates DNA-binding activities of this class of bZip proteins in transgenic tobacco plants. Our results demonstrate that the loss of TGA DNA-binding activities is correlated with suppression of two xenobiotic-responsive genes, GNT35 and STR246, and enhanced induction of pathogenesis-related (PR) genes by SA. In addition, these TGA-suppressed plants exhibited higher levels of PR gene induction by pathogen challenge and an enhanced SAR. These results suggest that TGA transcription factors serve both negative and positive regulatory roles in mediating plant defense responses.

Selection of a high-affinity DNA pool for a bZip protein with an out-of-phase alignment of the basic region relative to the leucine zipper

bZip transcription factors contain two regions that are required for DNA binding: a leucine zipper dimerization domain and a highly charged basic region that directly contacts DNA. The spacing between these subdomains is strictly conserved, and changes in this spacing result in a loss of function. Using an in vitro selection strategy, we have investigated the ability of a bZip protein with incorrect spacing between these two regions to bind specifically to DNA. Surprisingly, we find that although such a protein does not bind to its predicted site, it is possible to isolate a pool of DNAs that bind with very similar affinity to that of GCN4 for its optimum DNA site.

The E2A-HLF oncoprotein activates Groucho-related genes and suppresses Runx1.

The E2A-HLF fusion gene, formed by the t(17;19)(q22;p13) chromosomal translocation in leukemic pro-B cells, encodes a chimeric transcription factor consisting of the transactivation domain of E2A linked to the bZIP DNA-binding and protein dimerization domain of hepatic leukemia factor (HLF). This oncoprotein blocks apoptosis induced by growth factor deprivation or irradiation, but the mechanism for this effect remains unclear. We therefore performed representational difference analysis (RDA) to identify downstream genetic targets of E2A-HLF, using a murine FL5.12 pro-B cell line that had been stably transfected with E2A-HLF cDNA under the control of a zinc-regulated metallothionein promoter. Two RDA clones, designated RDA1 and RDA3, were differentially upregulated in E2A-HLF-positive cells after zinc induction. The corresponding cDNAs encoded two WD40 repeat-containing proteins, Grg2 and Grg6. Both are related to the Drosophila protein Groucho, a transcriptional corepressor that lacks DNA-binding activity on its own but can act in concert with other proteins to regulate embryologic development of the fly. Expression of both Grg2 and Grg6 was upregulated 10- to 50-fold by E2A-HLF. Immunoblot analysis detected increased amounts of two additional Groucho-related proteins, Grg1 and Grg4, in cells expressing E2A-HLF. A mutant E2A-HLF protein with a disabled DNA-binding region also mediated pro-B cell survival and activated Groucho-related genes. Among the transcription factors known to interact with Groucho-related protein, only RUNX1 was appreciably downregulated by E2A-HLF. Our results identify a highly conserved family of transcriptional corepressors that are activated by E2A-HLF, and they suggest that downregulation of RUNX1 may contribute to E2A-HLF-mediated leukemogenesis.

Effects of nucleic acids and polyanions on dimer formation and DNA binding by bZIP and bHLHZip transcription factors

A large fraction of known transcription factors form 2:1 complexes with DNA. In our studies of the assembly of such ternary (protein–protein–DNA) complexes formed by bZIP and bHLHZip proteins, we found that the proteins recognize DNA as monomers. Here we show that protein monomer–DNA complexes are favored at high DNA concentrations. Further, we show that, due to fast rates of association with protein monomers, DNA and other polyanions accelerate the rate of protein dimer formation. Finally, we find that DNA-assisted formation of protein dimers provides a mechanism by which dimeric transcription factors can rapidly discriminate between specific and nonspecific sites.

AR Suppresses Transcription of the α Glycoprotein Hormone Subunit Gene Through Protein-Protein Interactions with cJun and Activation Transcription Factor 2

Previously, we reported that the AR directly suppressed transcription of the alpha glycoprotein hormone subunit (alphaGSU) gene in a ligand-dependent fashion while ER had no effect. Mutagenesis studies of the alphaGSU promoter indicated that two elements were required for AR-mediated suppression: the alpha basal element and tandem cAMP response elements (CREs). Because several members of the bZip family of transcriptional proteins can bind the CREs, we used several functional assays to determine whether AR interacts selectively with cJun, activation transcription factor 2 (ATF2), or CRE binding protein (CREB). When tested by cotransfection with AR, cJun and ATF2 specifically rescued androgen-mediated suppression of the alphaGSU-reporter construct in a gonadotrope-derived cell line. In contrast, cotransfected CREB displayed no activity in this rescue assay. In fact, overexpression of CREB alone diminished activity of the alphaGSU promoter, suggesting that the transcriptional activity normally conferred by the tandem CREs in gonadotropes requires their occupancy by cJun/ATF2 heterodimers. Binding assays carried out with a glutathione-S-transferase-AR fusion protein indicated that the receptor itself also displayed a clear preference for binding cJun and ATF2. Furthermore, we ruled out the possibility that AR suppressed activity of the alphaGSU promoter by reducing synthesis of these bZip proteins. Additional experiments suggested that phosphorylation of AR or histone acetylation are unlikely requirements for AR suppression of alphaGSU promoter activity. Thus, our data suggest that AR suppresses activity of the alphaGSU promoter through direct protein-protein interactions with cJun and ATF2.

Electrostatic control of half-site spacing preferences by the cyclic AMP response element-binding protein CREB.

Basic region leucine zipper (bZIP) proteins represent a class of transcription factors that bind DNA using a simple, dimeric, alpha-helical recognition motif. The cAMP response element-binding protein (CREB) is a member of the CREB/ATF subfamily of bZIP proteins. CREB discriminates effectively in vivo and in vitro between the 10 bp cAMP response element (ATGACGTCAT, CRE) and the 9 bp activating protein 1 site (ATGACTCAT, AP-1). Here we describe an alanine scanning mutagenesis study designed to identify those residues within the CREB bZIP element that control CRE/AP-1 specificity. We find that the preference of CREB for the CRE site is controlled in a positive and negative way by acidic and basic residues in the basic, spacer and zipper segments. The CRE/AP-1 specificity of CREB is increased significantly by four glutamic acid residues located at positions 24, 28, 35 and 41; glutamic acid residues at positions 10 and 48 contribute in a more modest way. Specificity is decreased significantly by two basic residues located at positions 21 and 23; basic residues at positions 14, 18, 33 and 34 and V17 contribute in a more modest way. All of the residues that influence specificity significantly are located on the solvent-exposed face of the protein-DNA complex and likely participate in interactions between and among proteins, not between protein and DNA. The finding that the CRE/AP-1 specificity of CREB is dictated by the presence or absence of charged residues has interesting implications for how transcription factors seek and selectively bind sequences within genomic DNA.

Inhibition of major groove DNA binding bZIP proteins by positive patch polyamides

Cell permeable synthetic ligands that bind to predetermined DNA sequences offer a chemical approach to gene regulation, provided inhibition of a broad range of DNA transcription factors can be achieved. DNA minor groove binding polyamides containing aminoalkyl substituents at the N-1 of a single pyrrole residue display inhibitory effects for a bZIP protein which binds exclusively in the DNA major groove. For major groove protein inhibition, specific protein-DNA contacts along the phosphate backbone were targeted with the positively charged dimethylamino substituent on the backbone of a minor groove binding polyamide hairpin. Remarkably, these polyamides bind DNA with enhanced affinity and uncompromised specificity when compared to polyamides with the aminoalkyl moiety at the C-terminus. By adding bZIP transcription factors to the class of protein–DNA complexes that can be disrupted by minor groove binding ligands, these results may increase the functional utility of polyamides as regulators of gene expression.

Evidence for a disease-resistance pathway in rice similar to the NPR1-mediated signaling pathway in Arabidopsis.

The Arabidopsis NPR1/NIM1 gene is a key regulator of systemic acquired resistance (SAR). Over-expression of NPR1 leads to enhanced resistance in Arabidopsis. To investigate the role of NPR1 in monocots, we over-expressed the Arabidopsis NPR1 in rice and challenged the transgenic plants with Xanthomonas oryzae pv. oryzae (Xoo), the rice bacterial blight pathogen. The transgenic plants displayed enhanced resistance to Xoo. RNA blot hybridization indicates that enhanced resistance requires expression of NPR1 mRNA above a threshold level in rice. To identify components mediating the resistance controlled by NPR1, we used NPR1 as bait in a yeast two-hybrid screen. We isolated four cDNA clones encoding rice NPR1 interactors (named rTGA2.1, rTGA2.2, rTGA2.3 and rLG2) belonging to the bZIP family. rTGA2.1, rTGA2.2 and rTGA2.3 share 75, 76 and 78% identity with Arabidopsis TGA2, respectively. In contrast, rLG2 shares highest identity (81%) to the maize liguleless (LG2) gene product, which is involved in establishing the leaf blade-sheath boundary. The interaction of NPR1 with the rice bZIP proteins in yeast was impaired by the npr1-1 and npr1-2 mutations, but not by the nim1-4 mutation. The NPR1-rTGA2.1 interaction was confirmed by an in vitro pull-down experiment. In gel mobility shift assays, rTGA2.1 binds to the rice RCH10 promoter and to a cis-element required sequence-specifically for salicylic acid responsiveness. This is the first demonstration that the Arabidopsis NPR1 gene can enhance disease resistance in a monocot plant. These results also suggest that monocot and dicot plants share a conserved signal transduction pathway controlling NPR1-mediated resistance.

Functional Interaction of bZIP Proteins and the Large Subunit of Replication Factor C in Liver and Adipose Cells

The transcription factor CCAAT/enhancer-binding protein-alpha (C/EBPalpha) has a vital role in cell growth and differentiation. To delineate further a mechanism for C/EBPalpha-mediated differentiation, we screened C/EBPalpha-interacting proteins through far-Western screening. One of the strongest interactions was with RFC140, the large subunit of the replication factor C complex. C/EBPalpha specifically interacted with RFC140 from rat liver nuclear extract as determined by a combination of affinity chromatography and co-immunoprecipitation. Subsequent far-Western blotting showed that the bZIP domain of C/EBPalpha interacted with the DNA-binding region of RFC140. Overexpression of RFC140 in mammalian cells increased the transactivation activity of C/EBPalpha on both minimal and native promoters. Consistent with the enhanced transactivation, a complex of C/EBPalpha and RFC140 proteins with the cognate DNA element was detected in vitro. The specific interaction between C/EBPalpha and RFC140 was detected in the terminal differentiation of 3T3-L1 preadipocytes to adipocytes. The synergistic transcription effect of these two proteins increased the promoter activity and protein expression of peroxisome proliferator-activated receptor-gamma, which is a main regulator of adipocyte differentiation. Our results demonstrate that the specific transcription factor C/EBPalpha and the general DNA replication factor RFC140 interact functionally and physically. This observation highlights a unique mechanism by which the levels of the general replication factor can strongly modulate the functional activity of the specific transcription factor as a coactivator.

Induction of jlbA mRNA synthesis for a putative bZIP protein of Aspergillus nidulans by amino acid starvation.

The jlbA (jun-like hZIP) gene of Aspergillus nidulans was isolated. The deduced amino acid motif of the C-terminal region of jlhA encodes a putative DNA-binding site composed of a basic amino acid domain and an adjacent leucine zipper motif. This region shares highest similarities to the C-terminal DNA-binding domain and the basic zipper (bZIP)-motifs of transcription factors like CPCA from A. niger, Gcn4p from Saccharomyces cerevisiae, human JUNB and c-JUN. The putative jlbA protein contains a PEST-rich region (an instability region rich in the amino acids proline, glutamic acid, serine and threonine) described to be implicated in protein stability. The jlbA mRNA formation is elevated up to 40-fold upon amino acid starvation induced by the addition of the false feedback inhibitor 3-amino-1,2,4-triazole. This induction is partially dependent and partially independent on the presence of the transcription factor CPCA. Therefore jlbA is a novel gene of A. nidulans which is transcriptionally activated by amino acid starvation conditions.