Primary structure of the Saccharomyces cerevisiae GAL4 gene

The plant-parasitic cyst nematode effector GLAND4 is a DNA-binding protein

Cyst nematodes are plant pathogens that infect a wide range of economically important crops. One parasitic mechanism employed by cyst nematodes is the production and in planta delivery of effector proteins to modify plant cells and suppress defences to favour parasitism. This study focuses on GLAND4, an effector of Heterodera glycines and H. schachtii, the soybean and sugar beet cyst nematodes, respectively. We show that GLAND4 is recognized by the plant cellular machinery and is transported to the plant nucleus, an organelle for which little is known about plant nematode effector functions. We show that GLAND4 has DNA-binding ability and represses reporter gene expression in a plant transcriptional assay. One DNA fragment that binds to GLAND4 is localized in an Arabidopsis chromosomal region associated with the promoters of two lipid transfer protein genes (LTP). These LTPs have known defence functions and are down-regulated in the nematode feeding site. When expressed in Arabidopsis, the presence of GLAND4 causes the down-regulation of the two LTP genes in question, which is also associated with increased susceptibility to the plant-pathogenic bacterium Pseudomonas syringae. Furthermore, overexpression of one of the LTP genes reduces plant susceptibility to H. schachtii and P. syringae, confirming that LTP repression probably suppresses plant defences. This study makes GLAND4 one of a small subset of characterized plant nematode nuclear effectors and identifies GLAND4 as the first DNA-binding, plant-parasitic nematode effector.

Spatial and temporal control of transgene expression in zebrafish

Transgenic zebrafish research has provided valuable insights into gene functions and cell behaviors directing vertebrate development, physiology, and disease models. Most approaches use constitutive transgene expression and therefore do not provide control over the timing or levels of transgene induction. We describe an inducible gene expression system that uses new tissue-specific zebrafish transgenic lines that express the Gal4 transcription factor fused to the estrogen-binding domain of the human estrogen receptor. We show these Gal4-ERT driver lines confer rapid, tissue-specific induction of UAS-controlled transgenes following tamoxifen exposure in both embryos and adult fish. We demonstrate how this technology can be used to define developmental windows of gene function by spatiotemporal-controlled expression of constitutively active Notch1 in embryos. Given the array of existing UAS lines, the modular nature of this system will enable many previously intractable zebrafish experiments.

Potassium channels in Drosophila: historical breakthroughs, significance, and perspectives

Drosophila has enabled important breakthroughs in K(+) channel research, including identification and fi rst cloning of a voltage-activated K(+) channel, Shaker, a founding member of the K(V)1 family. Drosophila has also helped in discovering other K(+) channels, such as Shab, Shaw, Shal, Eag, Sei, Elk, and also Slo, a Ca(2+) - and voltage-dependent K(+) channel. These findings have contributed significantly to our understanding of ion channels and their role in physiology. Drosophila continues to play an important role in ion channel studies, benefiting from an unparalleled arsenal of genetic tools and availability of tens of thousands of genetically modified strains. These tools allow deletion, expression, or misexpression of almost any gene in question with temporal and spatial control. The combination of these tools and resources with the use of forward genetic approach in Drosophila further enhances its strength as a model system. There are many areas in which Drosophila can further help our understanding of ion channels and their function. These include signaling pathways involved in regulating and modulating ion channels, basic information on channels and currents where very little is currently known, and the role of ion channels in physiology and pathology.

From pioneers to team players: TGA transcription factors provide a molecular link between different stress pathways

The plant immune system encompasses an arsenal of defense genes that is activated upon recognition of a pathogen. Appropriate adjustment of gene expression is mediated by multiple interconnected signal transduction cascades that finally control the activity of transcription factors. These sequence-specific DNA-binding proteins act at the interface between the DNA and the regulatory protein network. In 1989, tobacco TGA1a was cloned as the first plant transcription factor. Since then, multiple studies have shown that members of the TGA family play important roles in defense responses against biotrophic and necrotrophic pathogens and against chemical stress. Here, we review 22 years of research on TGA factors which have yielded both consistent and conflicting results.

Induction of 9-cis-epoxycarotenoid dioxygenase in Arabidopsis thaliana seeds enhances seed dormancy

Full understanding of mechanisms that control seed dormancy and germination remains elusive. Whereas it has been proposed that translational control plays a predominant role in germination, other studies suggest the importance of specific gene expression patterns in imbibed seeds. Transgenic plants were developed to permit conditional expression of a gene encoding 9-cis-epoxycarotenoid dioxygenase 6 (NCED6), a rate-limiting enzyme in abscisic acid (ABA) biosynthesis, using the ecdysone receptor-based plant gene switch system and the ligand methoxyfenozide. Induction of NCED6 during imbibition increased ABA levels more than 20-fold and was sufficient to prevent seed germination. Germination suppression was prevented by fluridone, an inhibitor of ABA biosynthesis. In another study, induction of the NCED6 gene in transgenic seeds of nondormant mutants tt3 and tt4 reestablished seed dormancy. Furthermore, inducing expression of NCED6 during seed development suppressed vivipary, precocious germination of developing seeds. These results indicate that expression of a hormone metabolism gene in seeds can be a sole determinant of dormancy. This study opens the possibility of developing a robust technology to suppress or promote seed germination through engineering pathways of hormone metabolism.

In silico analysis for transcription factors with Zn(II)(2)C(6) binuclear cluster DNA-binding domains in Candida albicans

A total of 6047 open reading frames in the Candida albicans genome were screened for Zn(II)₂C₆-type zinc cluster proteins (or binuclear cluster proteins) involved in DNA recognition. These fungal proteins are transcription regulators of genes involved in a wide range of cellular processes, including metabolism of different compounds such as sugars or amino acids, as well as multi-drug resistance, control of meiosis, cell wall architecture, etc. The selection criteria used in the sequence analysis were the presence of the CysX₂CysX₆CysX_5-16CysX₂CysX_6-8Cys motif and a putative nuclear localization signal. Using this approach, 70 putative Zn(II)₂C₆ transcription factors have been found in the genome of C. albicans.

Functional analysis of the activation domain of RF2a, a rice transcription factor

Rice transcription factor RF2a binds to the BoxII cis element of the promoter of rice tungro bacilliform virus and activates promoter expression. The acidic acid-rich domain of RF2a is a transcription activator and has been partially characterized (Dai et al., 2003). The RF2a acidic domain (A; amino acids 49-116) was fused with the synthetic zinc finger ZF-TF 2C7 and was co-introduced with a reporter gene into transgenic Arabidopsis plants. Expression of the reporter gene was increased up to seven times by the effector. In transient assays in tobacco BY-2 protoplasts, we identified a subdomain comprising amino acids 56-84 (A5) that was equally as effective as an activator as the entire acidic domain. A chemically inducible system was used to show determined that A and A5 domains are equally as effective in transcription activation as the well-characterized VP16 activation domain. Bioinformatics analyses revealed that the A5 domain is present only in b-ZIP transcription factors. In dicots, the A domain contains an insertion of four amino acids that is not present in monocot proteins. The A5 domain, and similar domains in other b-ZIP transcription factors, is predicted to form an anti-parallel beta sheet structure.

Functionality of the GAL4/UAS system in Tribolium requires the use of endogenous core promoters

Background

The red flour beetle Tribolium castaneum has developed into an insect model system second only to Drosophila. Moreover, as a coleopteran it represents the most species-rich metazoan taxon which also includes many pest species. The genetic toolbox for Tribolium research has expanded in the past years but spatio-temporally controlled misexpression of genes has not been possible so far.

Results

Here we report the establishment of the GAL4/UAS binary expression system in Tribolium castaneum. Both GAL4Δ and GAL4VP16 driven by the endogenous heat shock inducible promoter of the Tribolium hsp68 gene are efficient in activating reporter gene expression under the control of the Upstream Activating Sequence (UAS). UAS driven ubiquitous tGFP fluorescence was observed in embryos within four hours after activation while in-situ hybridization against tGFP revealed expression already after two hours. The response is quick in relation to the duration of embryonic development in Tribolium - 72 hours with segmentation being completed after 24 hours - which makes the study of early embryonic processes possible using this system. By comparing the efficiency of constructs based on Tribolium, Drosophila, and artificial core promoters, respectively, we find that the use of endogenous core promoters is essential for high-level expression of transgenic constructs.

Conclusions

With the established GAL4/UAS binary expression system, ectopic misexpression approaches are now feasible in Tribolium. Our results support the contention that high-level transgene expression usually requires endogenous regulatory sequences, including endogenous core promoters in Tribolium and probably also other model systems.

Regulated ethylene insensitivity through the inducible expression of the Arabidopsis etr1-1 mutant ethylene receptor in tomato

Ethylene serves as an important hormone controlling several aspects of plant growth and development, including fruit ripening and leaf and petal senescence. Ethylene is perceived following its binding to membrane-localized receptors, resulting in their inactivation and the induction of ethylene responses. Five distinct types of receptors are expressed in Arabidopsis (Arabidopsis thaliana), and mutant receptors have been described that repress ethylene signaling in a dominant negative manner. One such mutant, ethylene resistant1-1 (etr1-1), results in a strong ethylene-insensitive phenotype in Arabidopsis. In this study, regulated expression of the Arabidopsis etr1-1 in tomato (Solanum lycopersicum) was achieved using an inducible promoter. In the absence of the inducer, transgenic seedlings remained sensitive to ethylene, but in its presence, a state of ethylene insensitivity was induced, resulting in the elongation of the hypocotyl and root in dark-grown seedlings in the presence of ethylene, a reduction or absence of an apical hook, and repression of ethylene-inducible E4 expression. The level of ethylene sensitivity could be controlled by the amount of inducer used, demonstrating a linear relationship between the degree of insensitivity and etr1-1 expression. Induction of etr1-1 expression also repressed the epinastic response to ethylene as well as delayed fruit ripening. Restoration of ethylene sensitivity was achieved following the cessation of the induction. These results demonstrate the ability to control ethylene responses temporally and in amount through the control of mutant receptor expression.

Genetic approaches to studying adenosine-to-inosine RNA editing

Increasing proteomic diversity via the hydrolytic deamination of adenosine to inosine (A-to-I) in select mRNA templates appears crucial to the correct functioning of the nervous system in several model organisms, including Drosophila, Caenorabditis elegans, and mice. The genome of the fruitfly, Drosophila melanogaster, contains a single gene encoding the enzyme responsible for deamination, termed ADAR (for adenosine deaminase acting on RNA). The mRNAs that form the substrates for ADAR primarily function in neuronal signaling, and, correspondingly, deletion of ADAR leads to severe nervous system defects. While several ADAR enzymes are present in mice, the presence of a single ADAR in Drosophila, combined with the diverse genetic toolkit available to researchers and the wide range of ADAR target mRNAs identified to date, make Drosophila an ideal organism to study the genetic basis of A-to-I RNA editing. This chapter describes a variety of methods for genetically manipulating Drosophila A-to-I editing both in time and space, as well as techniques to study the molecular basis of ADAR-mRNA interactions. A prerequisite for experiments in this field is the ability to quantify the levels of editing in a given mRNA. Therefore, several commonly used methods for the quantification of editing levels will also be described.

Hansenula polymorpha NMR2 and NMR4, two new loci involved in nitrogen metabolite repression

In the yeast Hansenula polymorpha (Pichia angusta) nitrate assimilation is tightly regulated and subject to a dual control: nitrogen metabolite repression (NMR), triggered by reduced nitrogen compounds, and induction, elicited by nitrate itself. In a previous paper [Serrani, F., Rossi, B. and Berardi, E (2001) Nitrogen metabolite repression in Hansenula polymorpha: the nmrl-l mutation. Curr. Genet. 40, 243-250], we identified five loci (NMR1-NMR5) involved in NMR, and characterised one of them (NMR1), which likely identifies a regulatory factor. Here, we describe two more mutants, namely nmr2-1 and nmr4-1. The first one possibly identifies a regulatory factor involved in nitrogen metabolite repression by various nitrogen sources alternative to ammonium. The second one, apparently involved in ammonium assimilation, probably has sensor functions.

Modulation of F1 hybrid stature without altering parent plants through trans-activated expression of a mutated rice GAI homologue

Hybrid breeding, by taking advantage of heterosis, brings about many superior properties to the F1 progeny. However, some properties, such as increased plant height, are not desirable for agronomic purposes. To specifically counter the height increase associated with hybrid progeny, we employed an Arabidopsis model and tested a trans-activation system for specifically expressing a mutated GAI gene only in the F1 hybrid plants to reduce plant stature. A transcriptional activator, the Gal4 DNA-binding domain fused to the acidic activation domain of herpes simplex virus VP16 protein, driven by a maize ubiquitin promoter, was introduced in one parental line. A rice GAI homologue with an N-terminal deletion of the DELLA domain, driven by a promoter that is responsive to the transcriptional activator, was transferred into another parental line. After genetic crossing, trans-activation of the GAI mutant gene resulted in a dwarf phenotype. Over 50 pair-wise crosses between the parental lines were performed, and analyses suggested that the percentage of F1 progeny exhibiting dwarfism ranged from about 25% to 100%. Furthermore, the dwarfism trait introduced in F1 progeny did not seem to affect total seed yield. Our result suggests the feasibility of manipulating F1 hybrid progeny traits without affecting parent plants or the agronomic property of the progeny.

Progress toward an expanded eukaryotic genetic code

Expanding the eukaryotic genetic code to include unnatural amino acids with novel properties would provide powerful tools for manipulating protein function in eukaryotic cells. Toward this goal, a general approach with potential for isolating aminoacyl-tRNA synthetases that incorporate unnatural amino acids with high fidelity into proteins in Saccharomyces cerevisiae is described. The method is based on activation of GAL4-responsive HIS3, URA3, or lacZ reporter genes by suppression of amber codons in GAL4. The optimization of GAL4 reporters is described, and the positive and negative selection of active Escherichia coli tyrosyl-tRNA synthetase (EcTyrRS)/tRNA(CUA) is demonstrated. Importantly, both selections can be performed on a single cell and with a range of stringencies. This method will facilitate the isolation of a range of aminoacyl-tRNA synthetase (aaRS)/tRNA(CUA) activities from large libraries of mutant synthetases.

The CRG1 gene required for resistance to the singlet oxygen-generating cercosporin toxin in Cercospora nicotianae encodes a putative fungal transcription factor

The Cercospora nicotianae CRG1 gene is involved in cellular resistance to the perylenequinone toxin, cercosporin, that generates highly toxic singlet oxygen upon exposure to light. The entire open reading frame (ORF) of CRG1 was isolated and sequenced. The gene contains an ORF of 1950bp including a 65-bp intron. The predicted 650 amino acid CRG1 protein contains a Cys(6)Zn(2) binuclear cluster DNA-binding motif with homology to various fungal regulatory proteins, indicating that CRG1 may act functionally as a transcription activator. Targeted gene disruption of CRG1 resulted in mutants that are partially sensitive to cercosporin and reduced in cercosporin production. Genetic complementation revealed that CRG1 fully restored cercosporin resistance, but only slightly restored cercosporin production in a UV-derived mutant (CS10) containing a single nucleotide substitution in crg1. Complementation of a crg1-null mutant, however, yielded strains that are similar to the wild-type in both phenotypes. These results indicate that the transcription regulator CRG1 is involved in the activation of genes associated with cercosporin resistance and production in the fungus Cercospora nicotianae.

Regulation of constitutively expressed and induced cutinase genes by different zinc finger transcription factors in Fusarium solani f. sp. pisi (Nectria haematococca)

Cutin monomers, generated by the low levels of constitutively expressed cutinase, induce high levels of cutinase that can help pathogenic fungi to penetrate into the host through the cuticle whose major structural polymer is cutin. We cloned three highly homologous cutinase genes, cut1, cut2, and cut3, from Fusarium solani f. pisi (Nectria haematococca). Amino acid sequence deduced from the nucleotide sequence of cut1 and cut2/3 matched with that of the peptides from cutinase 1 and cutinase 2, respectively, isolated from F. solani pisi grown on cutin as the sole carbon source. Induction of beta-glucuronidase gene fused to the promoters of the cutinases integrated into F. solani pisi genome indicates that cut2 is constitutively expressed and induced under starvation, whereas cut1 is highly induced by cutin monomers. A palindrome binding protein (PBP) previously cloned binds only to palindrome 1 of cut1 promoter but not palindrome 1 of cut2/3 which contains two base substitutions. PBP is thought to interfere with the binding of CTF1 alpha, the transcription factor involved in induction, to cut1 promoter and thus keep cut1 gene repressed until induced by cutin monomers. Because PBP cannot bind palindrome 1 of cut2, this gene is not repressed. CTF1 alpha does not transactivate cut2 promoter. A new Cys(6)Zn(2) motif-containing transcription factor, CTF1 beta, that binds palindrome 2 was cloned and sequenced. In yeast, CTF1 beta transactivates cut2 promoter but not cut1 promoter unless its palindrome 1 is mutated, unlike CTF1 alpha which transactivates cut1. Thus, CTF1 beta is involved in the constitutive expression of cut2 that causes production of low levels of cutin monomers that strongly induce cut1 using CTF1 alpha as the transcription factor.

A new approach reveals syncytia within the visceral musculature ofDrosophila melanogaster

In order to reveal syncytia within the visceral musculature of Drosophila melanogaster, we have combined the GAL4/UAS system with the single-cell transplantation technique. After transplantation of single cells from UAS-GFP donor embryos into ubiquitously GAL4-expressing recipients, the expression of the reporter gene was exclusively activated in syncytia containing both donor- and recipient-derived nuclei. In the first trial, we tested the system in the larval somatic musculature, which is already known to consist of syncytia. By this means we could show that most of the larval somatic muscles are generated by clonally non-related cells. Moreover, using this approach we were able to detect syncytia within the visceral musculature – a tissue that has previously been described as consisting of mononuclear cells. Both the longitudinal visceral musculature of the midgut and the circular musculature of the hindgut consist of syncytia and persist through metamorphosis. This novel application of the transplantation technique might be a powerful tool to trace syncytia in any organism using the GAL4/UAS system.

Novel fungal transcriptional activators, Cmr1p of Colletotrichum lagenarium and pig1p of Magnaporthe grisea, contain Cys2His2 zinc finger and Zn(II)2Cys6 binuclear cluster DNA-binding motifs and regulate transcription of melanin biosynthesis genes in a developmentally specific manner

Colletotrichum lagenarium and Magnaporthe grisea are plant pathogenic fungi that produce melanin during the appressorial differentiation stage of conidial germination and during the late stationary phase of mycelial growth. Here, we report the identification of genes for two unique transcription factors, CMR1 (Colletotrichum melanin regulation) and PIG1 (pigment of Magnaporthe), that are involved in melanin biosynthesis. Both Cmr1p and Pig1p contain two distinct DNA-binding motifs, a Cys2His2 zinc finger motif and a Zn(II)2Cys6 binuclear cluster motif. The presence of both these motifs in a single transcriptional regulatory protein is unique among known eukaryotic transcription factors. Deletion of CMR1 in C. lagenarium caused a defect in mycelial melanization, but not in appressorial melanization. Also, cmr1Delta mutants do not express the melanin biosynthetic structural genes SCD1 and THR1 during mycelial melanization, although the expression of these two genes was not affected during appressorial melanization.

High dosage expression of a zinc finger protein, Grt1, suppresses a mutant of fission yeast slp1(+), a homolog of CDC20/p55CDC/Fizzy

Selective proteolysis at and after the onset of anaphase is a key cell cycle event required for sister chromatid separation as well as for exit from mitosis. It requires ubiquitination of substrates by Anaphase Promoting Complex(APC)/Cyclosome. Slp1, a WD-repeat protein, is a putative activator for APC in fission yeast. With another WD- repeat protein, Ste9/Srw1, it is thought to promote the proteolysis in a substrate-specific manner. We report here characterization of a temperature-sensitive (ts) slp1 mutant and its high-dosage suppressor, grt1(+). In cells arrested in metaphase, wild-type Slp1 was preferentially found in a complex with hyperphosphorylated Cut9 (subunit of APC), whereas the ts Slp1 protein, lacking the last 113 amino acids, failed to interact with Cut9. The temperature sensitivity was suppressed by high dosage expression of a zinc finger protein, Grt1. The ts slp1 mutant was unable to maintain the normal level of Grt1 protein. The reduction in the Grt1 level may be a primary defect since high dosage expression of grt1(+) rescues the slp1 mutant. The grt1-suppression had an additive effect to ste9 and wee1-50, both of which partially suppress the ts slp1 mutant. Therefore, grt1(+) would define an independent pathway that facilitates the function of Slp1.

cDNA cloning and genomic structure of three genes localized to human chromosome band 5q31 encoding potential nuclear proteins

Loss of a whole chromosome 5, or a del(5q), is a recurring abnormality in malignant myeloid diseases. By cytogenetic and molecular analyses, we delineated previously a 1- to 1.5-Mb region that is deleted in all patients with a del(5q). In our efforts to identify a myeloid tumor suppressor gene within the commonly deleted segment (CDS), we have cloned and characterized the genes encoding three putative nuclear proteins, each of which contains a bipartite nuclear localization signal (NLS). In addition, C5ORF5 contains a putative rhoGAP domain at the N-terminus, C5ORF6 has a proline-rich sequence near the N-terminus, and C5ORF7 has a zinc-finger domain that partially overlaps the NLS. All three genes are ubiquitously expressed and encode novel proteins. The C5ORF5 cDNA is 5.47 kb encoding a protein of 915 amino acids (aa) with a predicted molecular mass of approximately 105 kDa. C5ORF5 has 23 exons spanning over 27 kb. The C5ORF6 transcript is 4.1 kb encoding a protein of 392 aa with a predicted molecular mass of approximately 43 kDa. C5ORF6 has 5 exons and spans approximately 11 kb. The C5ORF7 cDNA is 6.3 kb and encodes a protein of 1417 aa with a predicted molecular mass of approximately 155 kDa. C5ORF7 has 24 exons spanning approximately 64 kb. All three genes were localized to the distal half of the CDS between D5S1983 and D5S500. We evaluated each as a candidate tumor suppressor gene by the analysis of myeloid leukemia cells from patients with -5/del(5q), but no inactivating mutations were identified.

A GAL4-like protein is involved in the switch between biotrophic and necrotrophic phases of the infection process of Colletotrichum lindemuthianum on common bean

Random insertional mutagenesis was conducted with the hemibiotrophic fungus Colletotrichum lindemuthianum, causal agent of common bean anthracnose. Nine mutants that were altered in their infection process on the host plant were generated. One of these, H433 is a nonpathogenic mutant able to induce necrotic spots on infected leaves rapidly. These spots are similar to those observed during the hypersensitive reaction. Cytological observations showed that the development of the mutant H433 is stopped at the switch between the biotrophic and the necrotrophic phases. This mutant carries two independent insertions of the transforming plasmid pAN7-1. Complementation studies using the wild-type genomic regions corresponding to the two insertions showed that one is responsible for the H433 phenotype. Sequencing analysis identified a single open reading frame that encoded a putative transcriptional activator belonging to the fungal zinc cluster (Zn[II](2)Cys(6)) family. The corresponding gene was designated CLTA1 (for C. lindemuthianum transcriptional activator 1). Expression studies showed that CLTA1 is expressed in low amounts during in vitro culture. Targeted disrupted strains were generated, and they exhibited the same phenotype as the original mutant H433. Complementation of these disrupted strains by the CLTA1 gene led to full restoration of pathogenicity. This study demonstrates that CLTA1 is both a pathogenicity gene and a regulatory gene involved in the switch between biotrophy and necrotrophy of the infection process of a hemibiotrophic fungus.

Structural and functional complexity of the genomic region controlling AK-toxin biosynthesis and pathogenicity in the Japanese pear pathotype of Alternaria alternata

The Japanese pear pathotype of Alternaria alternata produces host-specific AK-toxin and causes black spot of Japanese pear. Previously, a cosmid clone, pcAKT-1, was isolated that contains two genes, AKT1 and AKT2, within a 5.0-kb region required for AK-toxin biosynthesis. The wild-type strain has multiple, nonfunctional copies of these genes. In the present study, two additional genes, AKTR-1 and AKT3-1, downstream of AKT2 were identified. Transformation of the wild type with AKTR-1- and AKT3-1-targeting vectors produced toxin-deficient (Tox-), nonpathogenic mutants. DNA gel blot analysis, however, demonstrated that the fragments targeted in Tox- mutants were different from those containing AKTR-1 and AKT3-1 on the transforming vectors. A cosmid clone, pcAKT-2, containing the targeted DNA was isolated and shown to carry two genes, AKTR-2 and AKT3-2, with high similarity to AKTR-1 and AKT3-1, respectively. Transcripts from not only AKTR-2 and AKT3-2 but also AKTR-1 and AKT3-1 were found in the wild type. DNA gel blot analysis with pulsed-field gel electrophoresis showed that AKT1, AKT2, AKT3, and AKTR and their homologues are on a single chromosome. These results indicate the structural and functional complexity of the genomic region controlling AK-toxin biosynthesis.

An in vivo assay for the identification of target proteases which cleave membrane-associated substrates

Proteases not only play a fundamental role in numerous physiological processes, but are also involved in several human diseases including Alzheimer's disease (AD). A key protease implicated in AD is the so far unidentified gamma-secretase, which cleaves the membrane-bound beta-amyloid precursor protein (betaAPP) at the C-terminus of its amyloid domain within the membrane to release the neurotoxic amyloid beta-peptide. In order to allow the isolation of proteases, which specifically cleave membrane-bound substrates within or in the vicinity of a transmembrane domain, we developed a reporter gene assay in Saccharomyces cerevisiae. This assay may allow the identification of genes encoding target proteases that specifically cleave membrane bound substrates by transforming expression libraries.

The hexokinase 2 protein participates in regulatory DNA-protein complexes necessary for glucose repression of the SUC2 gene in Saccharomyces cerevisiae

The HXK2 gene plays an important role in glucose repression in the yeast Saccharomyces cerevisiae. Recently we have described that the HXK2 gene product, isoenzyme 2 of hexokinase, is located both in the nucleus and in the cytoplasm of S. cerevisiae cells. In this work we used deletion analysis to identify the essential part of the protein-mediating nuclear localisation. Determinations of fructose-kinase activity and immunoblot analysis using anti-Hxk2 antibodies in isolated nuclei, together with observations of the fluorescence distribution of Hxk2-GFP fusion protein in cells transformed with an HXK2::gfp mutant gene, indicated that the decapeptide KKPQARKGSM, located between amino acid residues 7 and 16 of hexokinase 2, is important for nuclear localisation of the protein. Further experimental evidence, measuring invertase activity in wild-type and mutant cells expressing a truncated version of the Hxk2 protein unable to enter the nucleus, shows that a nuclear localisation of Hxk2 is necessary for glucose repression signalling of the SUC2 gene. Furthermore, we demonstrate using gel mobility shift analysis that Hxk2 participates in DNA-protein complexes with cis-acting regulatory elements of the SUC2 gene promoter.

AvrXa10 contains an acidic transcriptional activation domain in the functionally conserved C terminus

The avrXa10 gene of Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight of rice, is a member of the avrBs3 avirulence gene family and directs the elicitation of resistance in a gene-for-gene manner on rice lines carrying the resistance gene Xa10. The carboxyl (C) terminus of AvrXa10 has a previously undescribed domain that is structurally similar to the acidic activation domain of many eukaryotic transcription factors in addition to three nuclear localization signal (NLS) sequences. Removal of the C-terminal 38 codons containing the putative activation domain, but retaining the NLS sequences, was concomitant with the loss of avirulence activity. The C-terminal coding regions of avrBs3 and avrXa7 can be replaced by the corresponding region of avrXa10, and the genes retained specificity for the resistance genes Bs3 in pepper and Xa7 in rice, respectively. The avrBs3 and avrXa7 avirulence activities of the hybrid genes were also lost upon removal of the terminal 38 codons. When fused to the coding sequence of the Gal4 DNA binding domain, AvrXa10 activated transcription in yeast and Arabidopsis thaliana. Removal of the carboxyl region severely reduced transcriptional activation. AvrXa10 would have to be localized to the host cell nucleus to function autonomously in transcriptional activation. Consistent with this requirement, mutations in all three NLS sequences of avrXa10 caused a loss in avirulence activity. The findings demonstrate the requirement of the C terminus for AvrXa10 function and the potential for the members of this family of avirulence gene products to enter the host nucleus and alter host transcription.

The fluffy gene of Neurospora crassa encodes a Gal4p-type C6 zinc cluster protein required for conidial development

Neurospora crassa fluffy (fl) mutants are unable to produce macroconidia. We cloned the fl gene to determine its role in regulating conidiation. A cosmid clone containing fl was identified by complementation. The sequence of fl revealed that it encodes a Gal4p-type C6 zinc cluster protein with greatest similarity to the N. crassa NIT4 protein that regulates genes required for nitrate utilization. Analysis of several fl mutant alleles demonstrated that null mutants are blocked in the budding phase of development required to produce conidiophores. fl mRNA is transiently induced just prior to the developmental commitment to budding growth. This timing of fl expression is consistent with a role for FL protein in activation of the previously characterized conidiation-specific (con) genes, con-6 and con-10. These data suggest that FL acts as a developmentally regulated transcription factor required for conidiophore morphogenesis.

Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain

Gal4, a yeast protein, activates transcription of genes required for metabolism of galactose and melibiose. It binds as a dimer to a consensus palindromic 17-base pair DNA sequence. It is a member of the third family of proteins that contain zinc-mediated peptide loops that interact specifically with nucleic acids. Gal4 has a very distinctive zinc coordination profile and mode of DNA-binding. Here, we report the creation of a novel site-specific endonuclease by linking the N-terminal 147 amino acids of Gal4 to the cleavage domain of FokI endonuclease. The fusion protein is active and under optimal conditions, binds to a 17 bp consensus DNA site and cleaves near this site. As expected, the cleavage occurs on either side of the consensus binding site(s).

In vivo nuclear transport kinetics in Saccharomyces cerevisiae

We have described a direct fluorescence assay to measure the relative rates of NLS-directed import and passive export of an NLS-GFP fusion protein in yeast. The design and construction of the reporter GFP fusion, its spectral qualities, size, use of inducible promoters, and the choice of NLS, are variables that could extend the method's utility. Future applications will almost certainly demand the quantification of transport rates in single cells using image analysis techniques. As is the case whenever cellular processes are studied in vivo, the in vivo nuclear trafficking properties of NLS-GFP are complicated and poorly understood. Some will be attracted to NLS-GFP kinetic assays simply because so little is known about the function and regulation of the transport apparatus in living cells. At the same time, the uncertainties that accompany in vivo work necessarily prevent the rigorous interpretation of data, which biochemists expect from experiments performed in vitro using highly purified enzymes.

The DNA binding domain of the A-MYB transcription factor is responsible for its B cell-specific activity and binds to a B cell 110-kDa nuclear protein

Expression studies as well as the use of transgenic animals have demonstrated that the A-MYB transcription factor plays central and specific role in the regulation of mature B cell proliferation and/or differentiation. Furthermore, it is highly expressed in Burkitt's lymphoma cells and may participate in the pathogenesis of this disease. We have therefore investigated the transcriptional activity of A-MYB and its regulation in several human lymphoid cell lines using co-transfection assays and show that A-MYB is transcriptionally active in all the B cell lines studied, but not in T cells. In particular the best responder cell line was the Burkitt's cell line Namalwa. The activity of A-MYB in B and not T cells was observed when either an artificial construct or the c-MYC promoter was used as a reporter. Furthermore, the functional domains responsible for DNA binding, transactivation, and negative regulation, previously characterized in a fibroblast context, were found to have similar activity in B cells. The region of A-MYB responsible for the B cell specific activity was defined to be the N-terminal 218 amino acids containing the DNA binding domain. Finally, a 110-kDa protein has been identified in the nuclei of all the B, but not T, cell lines that specifically binds to this A-MYB N-terminal domain. We hypothesize that this 110-kDa protein may be a functionally important B cell-specific co-activator of A-MYB.

Three genes encoding zinc finger proteins on human chromosome 6p21.3: members of a new subclass of the Kruppel gene family containing the conserved SCAN box domain

Five genes encoding zinc finger proteins of the Cys2His2 (or Krüppel) family were identified by direct cDNA hybridization to YACs 753H12 and 638D7, which encompass a region of human chromosome 6p21.3 extending from just centromeric of the microsatellite marker D6S306 to telomeric of D6S1260. The genes span a distance of approximately 1750 kb. The complete cDNA sequence, genomic structure, and tissue distribution of three of the zinc finger proteins, LD65/ZNF165, ZNF192 (previously called LD5-1), and ZNF193, are described. The three zinc finger proteins do not contain either Krüppel-associated box (KRAB) A or KRAB B domain, present in about one-third of all Krüppel-type zinc finger proteins (E. J. Bellefroid et al., 1991, Proc. Natl. Acad. Sci. USA 88: 3608-3612). The three zinc finger proteins do contain the conserved SCAN box domain (A. J. Williams et al., 1995, J. Biol. Chem. 270: 22143-22152). SCAN boxes are found in eight other genes in the GenBank database, five of which are also in the Kruppel family of zinc finger proteins lacking KRAB A and B domains and thereby define a new subclass of zinc finger proteins. In addition, three polymorphisms were identified in ZNF192, one of the zinc finger proteins. One of the three polymorphisms, Pro163Leu, is the second proline in a proline cluster (PEPP) in a region separating the SCAN box from the zinc finger motifs.

Gene transfer using a novel fusion protein, GAL4/invasin

The delivery of DNA to target cells using simple, defined, nonviral systems has become an area of intense interest in gene therapy. We describe here the development and characterization of one such novel system. A recombinant, bifunctional, fusion protein was expressed and purified from Escherichia coli. This protein consists of the DNA-binding domain of the yeast transcription factor GAL4 fused to the cell binding, internalization domain of the Yersinia pseudotuberculosis inv gene product, invasin. This protein, GAL4/Inv, together with poly-L-lysine, formed complexes with a chloramphenicol acetyltransferase (CAT) reporter plasmid that contains eight repeats of the GAL4 consensus recognition sequence. These complexes were shown to transfect target cells in an invasin receptor-dependent manner, resulting in transient CAT expression. A simple, targeted DNA delivery vehicle, as we describe here, represents a viable approach to nonviral gene delivery.

Evolution of a fungal regulatory gene family: the Zn(II)2Cys6 binuclear cluster DNA binding motif

The coevolution of DNA binding proteins and their cognate binding sites is essential for the maintenance of function. As a result, comparison of DNA binding proteins of unknown function in one species with characterized DNA binding proteins in another can identify potential targets and functions. The Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA binding domain has thus far been identified exclusively in fungal proteins, generally transcriptional regulators, and there are more than 80 known or predicted proteins which contain this motif, the best characterized of which are GAL4, PPR1, LEU3, HAP1, LAC9, and PUT3. Here we review all known proteins containing the Zn(II)2Cys6 motif, along with their function, DNA binding, dimerization, and zinc(II) coordination properties and DNA binding sites. In addition, we have identified all of the Zn(II)2Cys6 motif-containing proteins in the sequence databases, including a large number with unknown function from the completed Saccharomyces cerevisiae and ongoing Schizosaccharomyces pombe genome projects, and examined the phylogenetic relationships of all the Zn(II)2Cys6 motifs from these proteins. Based on these relationships, we have assigned potential functions to a number of these unknown proteins.

Cloning of cutinase transcription factor 1, a transactivating protein containing Cys6Zn2 binuclear cluster DNA-binding motif

Hydroxy fatty acids from plant cutin were shown previously to induce the expression of the cutinase gene via a palindromic sequence located at -159 base pairs of the cutinase gene in Fusarium solani f. sp. pisi (Nectria hematococca mating type VI). Of the two overlapping palindromes in this sequence, palindrome 2 was found to be essential for the inducibility of cutinase by hydroxy fatty acids. Screening of a phage expression library with the concatenated palindrome 2 as probe detected a distinct cDNA clone encoding a polypeptide designated cutinase transcription factor 1alpha (CTF1alpha) with a calculated molecular weight of 101,109. This protein contains a Cys6Zn2 binuclear cluster motif sharing homology to the Cys6Zn2 binuclear cluster DNA-binding domains of transcription factors from Saccharomyces cerevisiae, S. carlsbergensis, Kluyveromyces lactis, Neurospora crassa, Aspergillus nidulans, and A. flavus. CTF1alpha, expressed in Escherichia coli, showed specific binding to the palindrome 2 DNA fragment but not to palindrome 1 or mutant palindrome 2 DNA fragments, suggesting specific binding of CTF1alpha to palindrome 2. When CTF1alpha was expressed as a fusion protein with the nuclear localization sequence of SV40 in yeast, it transactivated the native cutinase promoter fused to the chloramphenicol acetyl transferase (cat) gene. Mutation of palindrome 2 but not palindrome 1 abolished this transactivation. Thus, CTF1alpha positively acts in vivo by binding selectively to palindrome 2 of the cutinase gene promoter.

Purification, identification, and properties of a Saccharomyces cerevisiae oleate-activated upstream activating sequence-binding protein that is involved in the activation of POX1

Peroxisomes have a central function in lipid metabolism, and it is well established that these organelles are inducible by many compounds including fatty acids. Peroxisomes are the sole site for the beta-oxidation of fatty acids in yeast. The first and rate-limiting enzyme of this cycle is fatty acyl-CoA oxidase. The gene encoding this enzyme in Saccharomyces cerevisiae (POX1) undergoes a complex regulation that is dependent on the growth environment. When this yeast is grown in medium containing oleic acid as the main carbon source, peroxisomes are induced and POX1 expression is activated. When cells are grown in the presence of glucose, the expression of POX1 mRNA is repressed, whereas growth on a carbon source such as glycerol or raffinose causes derepression. This rigorous regulation is brought about by the complex interactions between trans-acting factors and cis-elements in the POX1 promoter. Previously, we characterized regulatory elements in the promoter region of POX1 that are involved in the repression and activation of this gene (Wang, T., Luo, Y., and Small, G. M. (1994) J. Biol. Chem. 269, 24480-24485). In this study we have purified and identified an oleate-activated transcription factor (Oaf1p) that binds to the activating sequence (UAS1) in the POX1 gene. The protein has a predicted molecular mass of approximately 118 kDa.

Rab3 reversibly recruits rabphilin to synaptic vesicles by a mechanism analogous to raf recruitment by ras

GTP activates the interaction between the synaptic vesicle proteins rabphilin and rab3. This raises the question of whether rabphilin is a resident vesicle protein that recruits rab3 in a stage-dependent fashion, or if it is instead an effector protein recruited by rab3. We now show that rabphilin, like rab3, dissociates from synaptic vesicles after exocytosis in a manner requiring both Ca2+ and membrane fusion. Rabphilin interacts with GTP-rab3 via a N-terminal domain comprising a novel Zn2+(-)finger motif, and this interaction is essential for rabphilin binding to synaptic vesicles. Thus, in the same way that ras recruits raf to the plasma membrane, rab3 reversibly recruits rabphilin to synaptic vesicles in a stage-dependent manner. These results reveal an unexpected similarity between the molecular mechanisms by which small G protein function in recruiting effector proteins to membranes during membrane traffic and signal transduction.

Analysis of second-site mutations that suppress the multiple drug resistance phenotype of the yeast PDR1-7 allele

The yeast PDR1 locus encodes a member of the C6 zinc cluster family of transcriptional regulatory proteins. Among the targets of PDR1 is the yeast PDR5 locus. The product of this gene is a member of the ATP-binding cassette (ABC) transmembrane protein family and plays a major role in inhibitor efflux. Mutations in PDR1 affect the relative level of PDR5 transcript and can therefore result in increased or decreased drug resistance. We isolated three second-site suppressors of a PDR1-7 semidominant hyper-resistant mutation. These mutants were drug hypersensitive, as compared with isogenic controls. Two of the three mutations contained alterations in a putative DNA-binding domain. Significantly, the mutant proteins exhibited reduced DNA-binding capacity.

Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco

The Arabidopsis thaliana Athb-1 is a homeobox gene of unknown function. By analogy with homeobox genes of other organisms, its gene product, Athb-1, is most likely a transcription factor involved in developmental processes. We constructed a series of Athb-1-derived genes to examine the roles of Athb-1 in transcriptional regulation and plant development. Athb-1 was found to transactivate a promoter linked to a specific DNA binding site by transient expression assays. In transgenic tobacco plants, overexpression of Athb-1 or its chimeric derivatives with heterologous transactivating domains of the yeast transcription factor GAL4 or herpes simplex virus transcription factor VP16 conferred deetiolated phenotypes in the dark, including cotyledon expansion, true leaf development, and an inhibition of hypocotyl elongation. Expression of Athb-1 or the two chimeric derivatives also affected the development of palisade parenchyma under normal growth conditions, resulting in light green sectors in leaves and cotyledons, whereas other organs in the transgenic plants remained normal. Both developmental phenotypes were induced by glucocorticoid in transgenic plants expressing a chimeric transcription factor comprising the Athb-1 DNA binding domain, the VP16 transactivating domain, and the glucocorticoid receptor domain. Plants with severe inducible phenotypes showed additional abnormality in cotyledon expansion. Our results suggest that Athb-1 is a transcription activator involved in leaf development.

Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco

The Arabidopsis thaliana Athb-1 is a homeobox gene of unknown function. By analogy with homeobox genes of other organisms, its gene product, Athb-1, is most likely a transcription factor involved in developmental processes. We constructed a series of Athb-1-derived genes to examine the roles of Athb-1 in transcriptional regulation and plant development. Athb-1 was found to transactivate a promoter linked to a specific DNA binding site by transient expression assays. In transgenic tobacco plants, overexpression of Athb-1 or its chimeric derivatives with heterologous transactivating domains of the yeast transcription factor GAL4 or herpes simplex virus transcription factor VP16 conferred deetiolated phenotypes in the dark, including cotyledon expansion, true leaf development, and an inhibition of hypocotyl elongation. Expression of Athb-1 or the two chimeric derivatives also affected the development of palisade parenchyma under normal growth conditions, resulting in light green sectors in leaves and cotyledons, whereas other organs in the transgenic plants remained normal. Both developmental phenotypes were induced by glucocorticoid in transgenic plants expressing a chimeric transcription factor comprising the Athb-1 DNA binding domain, the VP16 transactivating domain, and the glucocorticoid receptor domain. Plants with severe inducible phenotypes showed additional abnormality in cotyledon expansion. Our results suggest that Athb-1 is a transcription activator involved in leaf development.

Sequence analysis of a 33.1 kb fragment from the left arm of Saccharomyces cerevisiae chromosome X, including putative proteins with leucine zippers, a fungal Zn(II)2-Cys6 binuclear cluster domain and a putative alpha 2-SCB-alpha 2 binding site

In the framework of the European BIOTECH project for sequencing the Saccharomyces cerevisiae genome, we have determined the nucleotide sequence of the left part of the cosmid clone 232 and the cosmid clone 233 provided by F. Galibert (Rennes Cedex, France). We present here 33,099 base pairs of sequence derived from the left arm of chromosome X of strain S288C. This sequence reveals 17 open reading frames (ORFs) with more than 299 base pairs, including the published sequences for ARG3, LIGTR/LIG1, ORF2, ACT3 and SCP160. Two other ORFs showed similarity with S. cerevisiae genes: one with the CAN1 gene coding for an arginine permease, and one with genes encoding the family of transcriptional activators containing a fungal Zn(II)2-Cys6 binuclear cluster domain like that found in Ppr1p or Ga14p. Both putative proteins contain a leucine zipper motif, the Can1p homologue has 12 putative membrane-spanning domains and a putative alpha 2-SCB-alpha 2 binding site. In a diploid disruption mutant of ORF J0922 coding for the transcriptional activator homologue, no colonies appeared before 10 days after transformation and then grew slowly. In contrast, haploid disruption mutants showed a growth phenotype like wild-type cells. One ORF showed weak similarity to the rad4 gene product of Schizosaccharomyces pombe and is essential for yeast growth. Five ORFs showed similarity to putative genes on the right arm of chromosome XI of S. cerevisiae. Two of them have similarity to each other and belong to a family of extracellular proteins that groups mammalian SCP/Tpx-1, insects Ag3/Ag5, plants PR-1 and fungi Sc7/Sc14.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparison of two b1 alleles from within the A mating-type of the basidiomycete Coprinus cinereus

We cloned and sequenced the b1 specificity gene, b1-2, from the A43 mating-type locus of the basidiomycete Coprinus cinereus, to compare its molecular structure to a previously published allele. The b1-2 gene was identified and isolated using a transformation assay for A-activity. The nucleotide (nt) sequence was determined and compared to the published sequence for the b1 specificity gene of the A42 mating-type locus. Both genes map to the same physical location within the A mating-type locus and conserved structural organization is observed at both the genomic and the protein level. Sequence alignments show that the two alleles share 73% overall nt sequence identity for the open reading frames (ORFs) and 68% overall amino acid (aa) sequence identity for the deduced polypeptides. Allowing for conservative substitutions, the overall aa sequence similarity is 79%. Comparison of the deduced aa sequences reveals several conserved structural motifs, including a DNA-binding homeodomain, putative bipartite nuclear localization signal sequences, and four predicted dimerization motifs. Regions rich in Pro and hydroxylated aa (Ser and Thr) are also common to both alleles. Sequence similarity varies greatly along the length of the gene at both the nt and aa levels. In general, similarity increases progressively from the N- to the C-terminal end with variable patterns of similarity observed for individual exons and the predicted motifs they encode. The low sequence similarity observed in the N terminus suggests that variability in this region may be involved in non-self recognition. Differing levels of positional and compositional constraint are apparent for different functional domains.

A novel cDNA, priBc, encoding a protein with a Zn(II)2Cys6 zinc cluster DNA-binding motif, derived from the basidiomycete Lentinus edodes

A cDNA clone (designated priBc) was isolated from a primordial cDNA library of the basidiomycete, Lentinus edodes (Le). The priBc clone consisted of 2628 bp encoding 565 amino acids. As was expected, the priB transcript was abundant in primordia, while preprimordial mycelia and mature fruiting bodies contained lower levels of this Le transcript. The deduced PRIB protein (64 kDa) contained a 'Zn(II)2Cys6 zinc cluster' DNA-binding motif. PRIB was produced in Escherichia coli using the bacteriophage T7 expression system. Southwestern blot analysis revealed that PRIB binds to the DNA fragment containing the upstream region of priB.

Cloning of two related genes encoding the 56-kDa and 123-kDa subunits of trehalose synthase from the yeast Saccharomyces cerevisiae

Preparations of intact trehalose synthase contain three polypeptides with molecular masses of 56, 102 and 123 kDa. We have cloned the genes TSS1 and TSL1 coding for the 56- and 123-kDa subunits, respectively. These genes are located on chromosomes II (TSS1) and XIII (TSL1). The TSS1 gene was found to be identical with CIF1, a gene required for normal growth on glucose. The product of the entire TSS1 gene exhibits 37% identity with a 502-amino-acid stretch from the middle of the TSL1 product. Disruption of the TSS1 gene in yeast eliminates both trehalose 6-phosphate synthase (Tre6P synthase) and trehalose 6-phosphate phosphatase (Tre6Pase) activities, and reintroduction of this gene restores these activities. Transformation of Escherichia coli with TSS1 increases its Tre6P synthase activity. Specific proteolytic degradation of the 123-kDa polypeptide from the N-terminus greatly influences the Tre6P synthase activity, decreasing its inhibition by phosphate and activatability by fructose 6-phosphate but has little effect on the Tre6Pase activity. These results suggest that this N-terminal part confers regulatory properties upon the Tre6P synthase activity.

cDNA cloning of a mouse factor that activates transcription from a metal response element of the mouse metallothionein-I gene in yeast

A cDNA that encodes a mouse factor that activates expression from a metal response element of the mouse metallothionein-I gene has been isolated by complementation cloning in yeast cells. The cDNA encodes a peptide with a maximum length of 99 amino acids that includes a single zinc finger sequence. In yeast cells, the cloned factor induces transcription from the metal response element in a sequence-specific but metal-independent fashion. The cDNA hybridizes to a 550-base mRNA that is constitutively expressed in mouse tissue culture cells. The ability of the mouse factor to activate transcription in yeast cells is dependent upon the carbon source.