Recognition of diverse sequences by class I zinc fingers: asymmetries and indirect effects on specificity in the interaction between CF2II and A+T-rich elements

A single C4 Zinc finger-containing protein from Litopenaeus vannamei involved in antibacterial responses

The Zinc finger domains (ZnFs), which contain finger-like protrusions stabilized by zinc ions and function to bind DNA, RNA, protein and lipid substrates, are ubiquitously present in a large number of proteins. In this study, a novel protein containing a single C4 type Znf domain (SZnf) was identified from Pacific white shrimp, Litopenaeus vannamei and its role in immunity was further investigated. The ZnF domain of SZnF but not other regions shared high homology with those of fushi tarazu-factor 1 (FTZ-F1) proteins. The SZnF protein was mainly localized in the cytoplasm and was also present in the nucleus at a small level. SZnF was high expressed in the scape and muscle tissues of healthy shrimp and its expression in gill and heptopancreas was strongly up-regulated during bacterial infection. Silencing of SZnf in vivo could strongly increase the susceptibility of shrimp to infection with Vibrio parahaemolyticus but not white spot syndrome virus (WSSV), suggesting that SZnf could be mainly involved in antibacterial responses. Both dual luciferase reporter assays and real-time PCR analysis demonstrated that SZnf could positively regulate the expression of various antimicrobial peptides in vitro and in vivo, which could be part of the mechanism underlying its antibacterial effects. In summary, the current study could help learn more about the function of ZnF-containing proteins and the regulatory mechanisms of immune responses against pathogen infection in crustaceans.

The complex spatio-temporal regulation of the Drosophila myoblast attractant gene duf/kirre

A key early player in the regulation of myoblast fusion is the gene dumbfounded (duf, also known as kirre). Duf must be expressed, and function, in founder cells (FCs). A fixed number of FCs are chosen from a pool of equivalent myoblasts and serve to attract fusion-competent myoblasts (FCMs) to fuse with them to form a multinucleate muscle-fibre. The spatial and temporal regulation of duf expression and function are important and play a deciding role in choice of fibre number, location and perhaps size. We have used a combination of bioinformatics and functional enhancer deletion approaches to understand the regulation of duf. By transgenic enhancer-reporter deletion analysis of the duf regulatory region, we found that several distinct enhancer modules regulate duf expression in specific muscle founders of the embryo and the adult. In addition to existing bioinformatics tools, we used a new program for analysis of regulatory sequence, PhyloGibbs-MP, whose development was largely motivated by the requirements of this work. The results complement our deletion analysis by identifying transcription factors whose predicted binding regions match with our deletion constructs. Experimental evidence for the relevance of some of these TF binding sites comes from available ChIP-on-chip from the literature, and from our analysis of localization of myogenic transcription factors with duf enhancer reporter gene expression. Our results demonstrate the complex regulation in each founder cell of a gene that is expressed in all founder cells. They provide evidence for transcriptional control—both activation and repression—as an important player in the regulation of myoblast fusion. The set of enhancer constructs generated will be valuable in identifying novel trans-acting factor-binding sites and chromatin regulation during myoblast fusion in Drosophila. Our results and the bioinformatics tools developed provide a basis for the study of the transcriptional regulation of other complex genes.

Intron loss is associated with gain of function in the evolution of the gloverin family of antibacterial genes in Bombyx mori

Gene duplication is a characteristic feature of eukaryotic genomes. Here we investigated the role of gene duplication in the evolution of the gloverin family of antibacterial genes (Bmglv1, Bmglv2, Bmglv3, and Bmglv4) in Bombyx mori. We observed the following two significant changes during the first duplication event: (i) loss of intronV, located in the 3'-untranslated region (UTR) of the ancestral gene Bmglv1, and (ii) 12-bp deletion in exon3. We show that loss of intronV during Bmglv1 to Bmglv2 duplication was associated with embryonic expression of Bmglv2. Gel mobility shift, chromatin immunoprecipitation, and immunodepletion assays identified chorion factor 2, a zinc finger protein, as the repressor molecule that bound to a 10-bp regulatory motif in intronV of Bmglv1 and repressed its transcription. gloverin paralogs that lacked intronV were independent of chorion factor 2 regulation and expressed in embryo. These results suggest that change in cis-regulation because of intron loss resulted in embryonic expression of Bmglv2-4, a gain of function over Bmglv1. Studies on the significance of intron loss have focused on introns present within the coding sequences for their potential effect on the open reading frame, whereas introns present in the UTRs of the genes were not given due attention. This study emphasizes the regulatory function of the 3'-UTR intron. In addition, we also studied the genomic loss and show that "in-frame" deletion of 12 nucleotides led to loss of amino acids IHDF resulting in the generation of a prepro-processing site in BmGlv2. As a result, the N-terminal pro-part of BmGlv2, but not of BmGlv1, gets processed in an infection-dependent manner suggesting that prepro-processing is an evolved feature in Gloverins.

CF2 activity and enhancer integration are required for proper muscle gene expression in Drosophila

The creation of the contractile apparatus in muscle involves the co-activation of a group of genes encoding muscle-specific proteins and the production of high levels of protein in a short period of time. We have studied the transcriptional control of six Drosophila muscle genes that have similar expression profiles and we have compared these mechanisms with those employed to control the distinct expression profiles of other Drosophila genes. The regulatory elements controlling the transcription of co-expressed muscle genes share an Upstream Regulatory Element and an Intronic Regulatory Element. Moreover, similar clusters of MEF2 and CF2 binding sites are present in these elements. Here, we demonstrate that CF2 depletion alters the relative expression of thin and thick filament components. We propose that the appropriate rapid gene expression responses during muscle formation and the maintenance of each muscle type is guaranteed in Drosophila by equivalent duplicate enhancer-like elements. This mechanism may be exceptional and restricted to muscle genes, reflecting the specific requirement to mediate rapid muscle responses. However, it may also be a more general mechanism to control the correct levels of gene expression during development in each cell type.

Myocyte enhancer factor 2 and chorion factor 2 collaborate in activation of the myogenic program in Drosophila

The process of myogenesis requires the coordinated activation of many structural genes whose products are required for myofibril assembly, function, and regulation. Although numerous reports have documented the importance of the myogenic regulator myocyte enhancer factor 2 (MEF2) in muscle differentiation, the interaction of MEF2 with cofactors is critical to the realization of muscle fate. We identify here a genomic region required for full MEF2-mediated activation of actin gene expression in Drosophila, and we identify the zinc finger transcriptional regulator chorion factor 2 (CF2) as a factor functioning alongside MEF2 via this region. Furthermore, although both MEF2 and CF2 can individually activate actin gene expression, we demonstrate that these two factors collaborate in regulating the Actin57B target gene in vitro and in vivo. More globally, MEF2 and CF2 synergistically activate the enhancers of a number of muscle-specific genes, and loss of CF2 function in vivo results in reductions in the levels of several muscle structural gene transcripts. These findings validate a general importance of CF2 alongside MEF2 as a critical regulator of the myogenic program, identify a new regulator functioning with MEF2 to control cell fate, and provide insight into the network of regulatory events that shape the developing musculature.

Co-operation between enhancers modulates quantitative expression from the Drosophila Paramyosin/miniparamyosin gene in different muscle types

The distinct muscles of an organism accumulate different quantities of structural proteins, but always maintaining their stoichiometry. However, the mechanisms that control the levels of these proteins and that co-ordinate muscle gene expression remain to be defined. The paramyosin/miniparamyosin gene encodes two thick filament proteins transcribed from two different promoters. We have analysed the regulatory regions that control expression of this gene and that are situated in the two promoters, the 5' and the internal promoters, both in vivo and in silico. A distal muscle enhancer containing three conserved MEF2 motifs is essential to drive high levels of paramyosin expression in all the major embryonic, larval and adult muscles. This enhancer shares sequence motifs, as well as its structure and organisation, with at least four co-regulated muscle enhancers that direct similar patterns of expression. However, other elements located downstream of the enhancer are also required for correct gene expression. Other muscle genes with different patterns of expression, such as miniparamyosin, are regulated by other basic mechanisms. The expression of miniparamyosin is controlled by two enhancers, AB and TX, but a BF modulator is required to ensure the correct levels of expression in each particular muscle. We propose a mechanism of transcriptional regulation in which similar enhancers are responsible for the spatio-temporal expression of co-regulated genes. However, it is the interaction between enhancers which ensures that the correct amounts of protein are expressed at any particular time in a cell, adapting these levels to their specific needs. These mechanisms may not be exclusive to neural or muscle tissue and might represent a general mechanism for genes that are spatially and temporally co-regulated.

Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors

We have developed a method in which randomized libraries of zinc finger-containing artificial transcription factors are used to induce phenotypic variations in yeast and mammalian cells. By linking multiple zinc-finger domains together, we constructed more than 100,000 zinc-finger proteins with diverse DNA-binding specificities and fused each of them to either a transcription activation or repression domain. The resulting transcriptional regulatory proteins were expressed individually in cells, and the transfected cells were screened for various phenotypic changes, such as drug resistance, thermotolerance or osmotolerance in yeast, and differentiation in mammalian cells. Genes associated with the selected phenotypes were also identified. Our results show that randomized libraries of artificial transcription factors are useful tools for functional genomics and phenotypic engineering.

Identification and mapping of the promoter for the gene encoding the ferritin heavy-chain homologue of the yellow fever mosquito Aedes aegypti

Mosquitoes are responsible for the transmission of numerous human diseases. The recent development of transgenic mosquitoes provides a new tool to examine molecular interactions between insect vectors and the pathogens they transmit. One focus in generating transgenic mosquito lies on expressing anti-pathogenic proteins at primary sites of pathogenic invasions, specifically the mosquito gut. Promoters that direct the expression of anti-pathogenic proteins in the mosquito gut are thus sought after because they may provide ways to hinder pathogenic development in the mosquito. Here, we report the identification and mapping of a strong promoter from the Aedes aegypti ferritin heavy-chain homologue (HCH) gene. All known insect ferritin HCH genes are expressed in the gut and inducible by an iron overload. Our transfection assays and DNase I footprinting analyses show that the mosquito ferritin HCH-gene contains regulatory elements both upstream and downstream of the transcriptional start site. The promoter of this gene contains a CF2 site, two GATA-binding sites, an E2F site, a TATA-box, an AP-1 site and a C/EBP binding site.

Novel strategy for the design of a new zinc finger: creation of a zinc finger for the AT-rich sequence by alpha-helix substitution

In this communication, a novel strategy for the design of a zinc finger peptide on the basis of alpha-helix substitution has been demonstrated. Sp1HM is a helix-substituted mutant for the wild-type Sp1(zf123) and its alpha-helix of each finger is replaced by that of fingers 4-6 of CF2-II. The circular dichroism spectrum of Sp1HM suggests that Sp1HM has an ordered secondary structure similar to that of Sp1(zf123). From the analyses of the DNA binding affinity and specificity by gel mobility shift assay, it is clearly indicated that Sp1HM specifically binds to the AT-rich sequence (5'-GTA TAT ATA-3') with 3.2 nM dissociation constants. Moreover, the zinc finger peptides for the sequence alternating between the AT- and GC-rich subsites can also be created by the alpha-helix substitution. This strategy is evidently effective and is also more convenient than the phage display method. Consequently, our design method is widely applicable to creating zinc finger peptides with novel binding specificities.

DNA binding and gene activation properties of the Nmp4 nuclear matrix transcription factors

Splice variants of the Nmp4 gene include nuclear matrix transcription factors that regulate the type I collagen alpha1(I) polypeptide chain (COL1A1) promoter and several matrix metalloproteinase (MMP) genes. To date, these are the only Cys(2)His(2) zinc finger proteins known to bind within the minor groove of homopolymeric (dA.dT) DNA. Nmp4 isoforms contain from 5 to 8 Cys(2)His(2) zinc fingers, an SH3-binding domain that overlaps with a putative AT-hook and a polyglutamine-alanine repeat (poly(QA)). To determine the mechanistic significance of Cys(2)His(2) zinc finger association with this unusual consensus DNA binding element, we identified the Nmp4 DNA-binding and transcriptional activation domains. Zinc fingers 2, 3, and 6 mediated association with the homopolymeric (dA.dT) COL1A1/MMP DNA consensus element. The N terminus of the Nmp4 protein exhibited a strong trans-activation capacity when fused to the GAL4 DNA-binding domain, but this activity was masked within the context of the full-length Nmp4-GAL4 DNA-binding domain chimera. However, upon binding to the COL1A1/MMP homopolymeric (dA.dT) element, the native Nmp4 protein up-regulated transcription, and the poly(QA) domain acquired a significant role in trans-activation. We propose that allosteric effects induced upon zinc finger association with the homopolymeric (dA.dT) minor groove confer context-specific functionality to this unusual family of Cys(2)His(2) transcription factors.

Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors

In previous studies we have developed Cys(2)-His(2) zinc finger domains that specifically recognized each of the 16 5'-GNN-3' DNA target sequences and could be used to assemble six-finger proteins that bind 18-base pair DNA sequences (Beerli, R. R., Dreier, B., and Barbas, C. F., III (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 1495--1500). Such proteins provide the basis for the construction of artificial transcription factors to study gene/function relationships in the post-genomic era. Central to the universal application of this approach is the development of zinc finger domains that specifically recognize each of the 64 possible DNA triplets. Here we describe the construction of a novel phage display library that enables the selection of zinc finger domains recognizing the 5'-ANN-3' family of DNA sequences. Library selections provided domains that in most cases showed binding specificity for the 3-base pair target site that they were selected to bind. These zinc finger domains were used to construct 6-finger proteins that specifically bound their 18-base pair target site with affinities in the pm to low nm range. When fused to regulatory domains, these proteins containing various numbers of 5'-ANN-3' domains were capable of specific transcriptional regulation of a reporter gene and the endogenous human ERBB-2 and ERBB-3 genes. These results suggest that modular DNA recognition by zinc finger domains is not limited to the 5'-GNN-3' family of DNA sequences and can be extended to the 5'-ANN-3' family. The domains characterized in this work provide for the rapid construction of artificial transcription factors, thereby greatly increasing the number of sequences and genes that can be targeted by DNA-binding proteins built from pre-defined zinc finger domains.

The artificial zinc finger coding gene 'Jazz' binds the utrophin promoter and activates transcription

Up-regulation of utrophin gene expression is recognized as a plausible therapeutic approach in the treatment of Duchenne muscular dystrophy (DMD). We have designed and engineered new zinc finger-based transcription factors capable of binding and activating transcription from the promoter of the dystrophin-related gene, utrophin. Using the recognition 'code' that proposes specific rules between zinc finger primary structure and potential DNA binding sites, we engineered a new gene named 'Jazz' that encodes for a three-zinc finger peptide. Jazz belongs to the Cys2-His2 zinc finger type and was engineered to target the nine base pair DNA sequence: 5'-GCT-GCT-GCG-3', present in the promoter region of both the human and mouse utrophin gene. The entire zinc finger alpha-helix region, containing the amino acid positions that are crucial for DNA binding, was specifically chosen on the basis of the contacts more frequently represented in the available list of the 'code'. Here we demonstrate that Jazz protein binds specifically to the double-stranded DNA target, with a dissociation constant of about 32 nM. Band shift and super-shift experiments confirmed the high affinity and specificity of Jazz protein for its DNA target. Moreover, we show that chimeric proteins, named Gal4-Jazz and Sp1-Jazz, are able to drive the transcription of a test gene from the human utrophin promoter.

Binding properties of the artificial zinc fingers coding gene Sint1

On the basis of the recognition "code" that suggests specific rules between zinc finger's primary structure and the finger's potential DNA binding sites, we have constructed a new three-zinc finger coding gene to target the nine base pair DNA sequence: 5'-TGG-ATG-GAC-3'. This artificial gene named "Sint1" belongs to the Cys2-His2 zinc finger type. The amino acid positions, crucial for DNA binding, have been specifically chosen on the basis of the amino acid/base contacts more frequently represented in the available list of the proposed recognition "code". Here we demonstrate that Sint1 protein binds specifically the double strand "code" DNA target, with a dissociation constant (Kd) comparable to the Kd of the well known Zif268 protein. Sint1 "code" deduced and the "experimental" selected DNA binding sites share five nucleotide positions. Interestingly, Sint1 shows both high affinity and specificity toward the single strand "code" DNA binding site, with a Kd comparable to the corresponding double strand DNA target. Moreover, we prove that Sint1 is able to bind RNA similarly to several natural zinc finger proteins.

Synthesis of a new zinc finger peptide; comparison of its 'code' deduced and 'CASTing' derived binding sites

Using two synthetic oligonucleotides, we have constructed a new gene containing three zinc finger motifs of the Cys2-His2 type. We named this artificial gene 'Mago'. The Mago nucleotide triplets encoding the amino acid positions, described to be crucial for DNA binding specificity, have been chosen on the basis of the proposed recognition 'code' that relates the zinc finger's primary structure to the DNA binding target. Here we demonstrate that Mago protein specifically binds the 'code' DNA target, with a dissociation constant (Kd) comparable to the Kd of the well known Zif268 protein with its binding site. Moreover, we show that the deduced Mago 'code' and the 'experimental' selected DNA binding sites are almost identical, differing only in two nucleotides at the side positions.

Recognition of DNA by single-chain derivatives of the phage 434 repressor: high affinity binding depends on both the contacted and non-contacted base pairs

Single-chain derivatives of the phage 434 repressor, termed single-chain repressors, contain covalently dimerized DNA-binding domains (DBD) which are connected with a peptide linker in a head-to-tail arrangement. The prototype RR69 contains two wild-type DBDs, while RR*69 contains a wild-type and an engineered DBD. In this latter domain, the DNA- contacting amino acids of thealpha3 helix of the 434 repressor are replaced by the corresponding residues of the related P22 repressor. We have used binding site selection, targeted mutagenesis and binding affinity studies to define the optimum DNA recognition sequence for these single-chain proteins. It is shown that RR69 recognizes DNA sequences containing the consensus boxes of the 434 operators in a palindromic arrangement, and that RR*69 optimally binds to non-palindromic sequences containing a 434 operator box and a TTAA box of which the latter is present in most P22 operators. The spacing of these boxes, as in the 434 operators, is 6 bp. The DNA-binding of both single-chain repressors, similar to that of the 434 repressor, is influenced indirectly by the sequence of the non-contacted, spacer region. Thus, high affinity binding is dependent on both direct and indirect recognition. Nonetheless, the single-chain framework can accommodate certain substitutions to obtain altered DNA-binding specificity and RR*69 represents an example for the combination of altered direct and unchanged indirect readout mechanisms.

A zinc finger directory for high-affinity DNA recognition

We have used two monovalent phage display libraries containing variants of the Zif268 DNA-binding domain to obtain families of zinc fingers that bind to alterations in the last 4 bp of the DNA sequence of the Zif268 consensus operator, GCG TGGGCG. Affinity selection was performed by altering the Zif268 operator three base pairs at a time, and simultaneously selecting for sets of 16 related DNA sequences. In this way, only four experiments were required to select for all possible 64 combinations of DNA triplet sequences. The results show that (i) for high-affinity DNA binding in the range observed for the Zif268 wild-type complex (Kd = 0.5-5 nM), finger 1 specifically requires the arginine at the carboxy terminus of its recognition helix that forms a bidentate hydrogen-bond with the guanine base (G) in the crystal structure of Zif268 complexed to its DNA operator sequence GCG TGG GCG; (ii) when the guanine base (G) is replaced by A, C, or T, a lower-affinity family (Kd > or = 50 nM) can be detected that shows an overall tendency to bind G-rich DNA; (iii) the residues at position 2 on the finger 2 recognition helix do not appear to interact strongly with the complementary 5' base in the finger 1 binding site; and (iv) unexpected substitutions at the amino terminus of finger 1 can occasionally result in specificity for the 3' base in the finger 1 binding site. A DNA recognition directory was constructed for high-affinity zinc fingers that recognize all three bases in a DNA triplet for seven sequences of the type GNN. Similar approaches may be applied to other zinc fingers to broaden the scope of the directory.