Sequence and nuclear localization of the Saccharomyces cerevisiae HAP2 protein, a transcriptional activator

MiR169 and its target PagHAP2-6 regulated by ABA are involved in poplar cambium dormancy

Dormancy is an effective strategy for perennial plants in temperate zones to survive the winter stress. MicroRNAs (miRNAs) have been well known as important regulators for various biological processes. In this study, we checked the expression of miR169 members in the cambium zone during dormancy and active growth in poplar and found that they had distinct expression patterns. We identified and characterized a dormancy-specific target gene of miR169, PagHAP2-6. 5' RACE assays confirmed the direct cleavage of PagHAP2-6 mRNA by miR169. The yeast functional complementation analysis showed that PagHAP2-6 was a homolog of Heme Activator Protein2 (HAP2)/Nuclear factor Y-A (NF-YA) transcription factor in poplar. qRT-PCR analysis indicated that PagHAP2-6 was highly expressed in the dormant stage, which was converse to the expression pattern of pag-miR169a, n, and r. In addition, the transcription of PagHAP2-6 was induced by exogenous abscisic acid (ABA), and both over-expression of PagHAP2-6 in Arabidopsis and transient co-expression assays in Nicotiana benthamiana indicated that PagHAP2-6 could increase the resistance to exogenous ABA. Taken together, the results suggested that miR169 and its target PagHAP2-6 regulated by ABA were involved in poplar cambium dormancy, which provided new insights into the regulatory mechanisms of tree dormancy-active growth transition.

ptr-MIR169 is a posttranscriptional repressor of PtrHAP2 during vegetative bud dormancy period of aspen (Populus tremuloides) trees

Dormancy is a mechanism evolved in woody perennial plants to survive the winter freezing and dehydration stress via temporary suspension of growth. We have identified two aspen microRNAs (ptr-MIR169a and ptr-MIR169h) which were highly and specifically expressed in dormant floral and vegetative buds. ptr-MIR169a and its target gene PtrHAP2-5 showed inverse expression patterns during the dormancy period. ptr-MIR169a transcript steadily increased through the first half of the dormancy period and gradually declined with the approach of active growing season. PtrHAP2-5 abundance was higher in the beginning of the dormancy period but rapidly declined thereafter. The decline of PtrHAP2-5 correlated with the high levels of ptr-MIR169a accumulation, suggesting miR169-mediated attenuation of the target PtrHAP2-5 transcript. We experimentally verified the cleavage of PtrHAP2-5 at the predicted miR169a site at the time when PtrHAP2-5 transcript decline was observed. HAP2 is a subunit of a nuclear transcription factor Y (NF-Y) complex consisting of two other units, HAP3 and HAP5. Using digital expression profiling we show that poplar HAP2 and HAP5 are preferentially detected in dormant tissues. Our study shows that microRNAs play a significant and as of yet unknown and unstudied role in regulating the timing of bud dormancy in trees.

NF-Y and the transcriptional activation of CCAAT promoters

The CCAAT box promoter element and NF-Y, the transcription factor (TF) that binds to it, were among the first cis-elements and trans-acting factors identified; their interplay is required for transcriptional activation of a sizeable number of eukaryotic genes. NF-Y consists of three evolutionarily conserved subunits: a dimer of NF-YB and NF-YC which closely resembles a histone, and the "innovative" NF-YA. In this review, we will provide an update on the functional and biological features that make NF-Y a fundamental link between chromatin and transcription. The last 25 years have witnessed a spectacular increase in our knowledge of how genes are regulated: from the identification of cis-acting sequences in promoters and enhancers, and the biochemical characterization of the corresponding TFs, to the merging of chromatin studies with the investigation of enzymatic machines that regulate epigenetic states. Originally identified and studied in yeast and mammals, NF-Y - also termed CBF and CP1 - is composed of three subunits, NF-YA, NF-YB and NF-YC. The complex recognizes the CCAAT pentanucleotide and specific flanking nucleotides with high specificity (Dorn et al., 1997; Hatamochi et al., 1988; Hooft van Huijsduijnen et al, 1987; Kim & Sheffery, 1990). A compelling set of bioinformatics studies clarified that the NF-Y preferred binding site is one of the most frequent promoter elements (Suzuki et al., 2001, 2004; Elkon et al., 2003; Mariño-Ramírez et al., 2004; FitzGerald et al., 2004; Linhart et al., 2005; Zhu et al., 2005; Lee et al., 2007; Abnizova et al., 2007; Grskovic et al., 2007; Halperin et al., 2009; Häkkinen et al., 2011). The same consensus, as determined by mutagenesis and SELEX studies (Bi et al., 1997), was also retrieved in ChIP-on-chip analysis (Testa et al., 2005; Ceribelli et al., 2006; Ceribelli et al., 2008; Reed et al., 2008). Additional structural features of the CCAAT box - position, orientation, presence of multiple Transcriptional Start Sites - were previously reviewed (Dolfini et al., 2009) and will not be considered in detail here.

Cytochrome P450 regulation: the interplay between its heme and apoprotein moieties in synthesis, assembly, repair, and disposal

Heme is vital to our aerobic universe. Heme cellular content is finely tuned through an exquisite control of synthesis and degradation. Heme deficiency is deleterious to cells, whereas excess heme is toxic. Most of the cellular heme serves as the prosthetic moiety of functionally diverse hemoproteins, including cytochromes P450 (P450s). In the liver, P450s are its major consumers, with >50% of hepatic heme committed to their synthesis. Prosthetic heme is the sine qua non of P450 catalytic biotransformation of both endo- and xenobiotics. This well-recognized functional role notwithstanding, heme also regulates P450 protein synthesis, assembly, repair, and disposal. These less well-appreciated aspects are reviewed herein.

Cloning and sequencing of a rice (Oryza sativa L.) RAPB cDNA using yeast one-hybrid system

Cis-acting elements containing CCAAT core sequence are located in 5' upstream regions of numerous eukaryotic genes. CCAAT-binding factors interact with thesecis acting elements as heteromeric complex and therefore control the gene transcription. CCAAT binding factors contain at least three subunits and each subunit alone cannot bind to CCAAT box. The cloning of a rice cDNA called RAPB which homologizes to yeast HAP2 (one of the subunits in CCAAT-binding factors) using yeast one-hybrid system and functional complementation approaches is reported. The analytic results indicate that the deduced amino acid sequence in the C terminal of RAPB also contains the functional domain of 60 amino acids highly homologous with yeast HAP2, whereas the deduced amino acids in N terminal region differs significantly, and no Gln-rich region is found in the RAPB protein as in HAP2. The Southern blotting analysis demonstrates that only one copy of RAPB gene exists in rice genome.

Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum

Nuclear Factor Y (NF-Y) is a trimeric complex that binds to the CCAAT box, a ubiquitous eukaryotic promoter element. The three subunits NF-YA, NF-YB and NF-YC are represented by single genes in yeast and mammals. However, in model plant species (Arabidopsis and rice) multiple genes encode each subunit providing the impetus for the investigation of the NF-Y transcription factor family in wheat. A total of 37 NF-Y and Dr1 genes (10 NF-YA, 11 NF-YB, 14 NF-YC and 2 Dr1) in Triticum aestivum were identified in the global DNA databases by computational analysis in this study. Each of the wheat NF-Y subunit families could be further divided into 4-5 clades based on their conserved core region sequences. Several conserved motifs outside of the NF-Y core regions were also identified by comparison of NF-Y members from wheat, rice and Arabidopsis. Quantitative RT-PCR analysis revealed that some of the wheat NF-Y genes were expressed ubiquitously, while others were expressed in an organ-specific manner. In particular, each TaNF-Y subunit family had members that were expressed predominantly in the endosperm. The expression of nine NF-Y and two Dr1 genes in wheat leaves appeared to be responsive to drought stress. Three of these genes were up-regulated under drought conditions, indicating that these members of the NF-Y and Dr1 families are potentially involved in plant drought adaptation. The combined expression and phylogenetic analyses revealed that members within the same phylogenetic clade generally shared a similar expression profile. Organ-specific expression and differential response to drought indicate a plant-specific biological role for various members of this transcription factor family.

Interaction of HapX with the CCAAT-binding complex--a novel mechanism of gene regulation by iron

Iron homeostasis requires subtle control systems, as iron is both essential and toxic. In Aspergillus nidulans, iron represses iron acquisition via the GATA factor SreA, and induces iron-dependent pathways at the transcriptional level, by a so far unknown mechanism. Here, we demonstrate that iron-dependent pathways (e.g., heme biosynthesis) are repressed during iron-depleted conditions by physical interaction of HapX with the CCAAT-binding core complex (CBC). Proteome analysis identified putative HapX targets. Mutual transcriptional control between hapX and sreA and synthetic lethality resulting from deletion of both regulatory genes indicate a tight interplay of these control systems. Expression of genes encoding CBC subunits was not influenced by iron availability, and their deletion was deleterious during iron-depleted and iron-replete conditions. Expression of hapX was repressed by iron and its deletion was deleterious during iron-depleted conditions only. These data indicate that the CBC has a general role and that HapX function is confined to iron-depleted conditions. Remarkably, CBC-mediated regulation has an inverse impact on the expression of the same gene set in A. nidulans, compared with Saccharomyces cerevisae.

Respirofermentative metabolism in Kluyveromyces lactis: Insights and perspectives

Yeasts do not form a homogeneous group as far as energy-yielding metabolism is concerned and the fate of pyruvate, a glycolytic intermediate, determines the type of energy metabolism. Kluyveromyces lactis has become an alternative to the traditional yeast Saccharomyces cerevisiae owing to its industrial applications as well as to studies on mitochondrial respiration. In this review we summarize the current knowdeledge about the K. lactis respirofermentative metabolism, taking into account the respiratory capacity of this yeast and the molecular mechanisms controlling its regulation, giving an up-to-date picture.

Heme: a regulator of rat hepatic tryptophan 2,3-dioxygenase?

The hepatic cytosolic hemoprotein tryptophan 2,3-dioxygenase (TDO) is the rate-limiting enzyme in tryptophan catabolism and thus plays a key role in regulating the physiological flux of tryptophan into relevant metabolic pathways. The TDO protein is induced by corticosteroids such as dexamethasone (DEX) and is stabilized by its prosthetic heme. In rats, acute chemically induced hepatic heme depletion reduces the functional hepatic TDO levels to 25-30% of basal levels within 1 h, and this decrease persists beyond 28 h of heme depletion at which time only 25-30% of the protein is available for heme incorporation. Since this could stem from impaired de novo synthesis and/or instability of the newly synthesized apoTDO protein in the absence of heme, we examined the specific role of heme in these events in a previously validated rat model of acute hepatic heme depletion triggered by the P450 suicide substrate 3, 5-dicarbethoxy 2,6-dimethyl-4-ethyl-1,4-dihydropyridine. We now show that exogenous heme can reverse the functional impairment of the enzyme observed during hepatic heme depletion and fully restore the impaired DEX-mediated induction of the enzyme to normal. Furthermore, through Northern/slot blot analyses coupled with nuclear run-on studies, we now document that this heme regulation of TDO is exerted primarily at the transcriptional level. Immunoblotting analyses also reveal corresponding changes in the TDO protein, thereby establishing that heme is necessary for DEX-inducible TDO mRNA transcription and subsequent translation. Thus, the TDO gene may contain heme-regulatory elements in addition to the reported glucocorticoid-responsive elements. Together, these findings suggest that clinically, hepatic heme deficiency may enhance the tryptophan flux into synthetic (serotonergic) pathways, not only by depriving prosthetic heme for a functionally competent TDO hemoprotein, its primary catabolic enzyme, but also by impairing the de novo synthesis of this enzyme.

Xenopus NF-Y pre-sets chromatin to potentiate p300 and acetylation-responsive transcription from the Xenopus hsp70 promoter in vivo

We identify Xenopus NF-Y as a key regulator of acetylation responsiveness for the Xenopus hsp70 promoter within chromatin assembled in Xenopus oocyte nuclei. Y-box sequences are required for the assembly of DNase I-hypersensitive sites in the hsp70 promoter, and for transcriptional activation both by inhibitors of histone deacetylase and by the p300 acetyltransferase. The viral oncoprotein E1A interferes with both of these activation steps. We clone Xenopus NF-YA, NF-YB and NF-YC and establish that NF-Y is the predominant Y-box-binding protein in Xenopus oocyte nuclei. NF-Y interacts with p300 in vivo and is itself a target for acetylation by p300. Transcription from the hsp70 promoter in chromatin can be enhanced further by heat shock factor. We suggest two steps in chromatin modification at the Xenopus hsp70 promoter: first the binding of NF-Y to the Y-boxes to pre-set chromatin and second the recruitment of p300 to modulate transcriptional activity.

Glutamine-rich domains activate transcription in yeast Saccharomyces cerevisiae

Activation domains of eukaryotic transcription factors can be classified into at least three distinct types based on their amino acid composition: acidic, proline-rich, and glutamine-rich. Acidic activators, such as yeast GAL4 and GCN4 and herpes simplex virus VP16, have been shown to stimulate transcription in various higher and lower eukaryotic cells. Similarly, proline-rich activators also function in both mammalian and yeast cells. These activators are regarded to possess "universal" activating potentials. By contrast, several studies have suggested that glutamine-rich activators such as human Sp1 are active in higher (mammalian) but not lower (yeast) eukaryotic cells. One interpretation is that lower eukaryotic cells lack a critical co-factor necessary for a glutamine-rich domain. This reasoning is counter-intuitive because many native yeast activator proteins contain glutamine-rich domains. Here, we have investigated the activity of a glutamine-rich GAL4-Sp1 domain A (Sp1A) hybrid protein in yeast Saccharomyces cerevisiae. We show that GAL4-Sp1A activated a GAL1-lacZ reporter by more than 200-fold over basal when the reporter was carried on a 2mu vector. The generality of the Sp1A results is supported by our finding that yeast glutamine-rich domains from HAP2 and MCM1 are also transcriptionally active in S. cerevisiae. Interestingly, we found that glutamine-rich domains are considerably less potent when responsive promoters (i.e. GAL1-lacZ) are integrated into yeast chromosome. Thus our results segregate the inherent transcriptional activity of a glutamine-rich domain in yeast S. cerevisiae from its apparent lack of activity when assayed on chromosomally embedded promoters.

Conservation and divergence of NF-Y transcriptional activation function

The CCAAT-binding protein NF-Y is involved in the regulation of a variety of eukaryotic genes and is formed in higher eukaryotes by three subunits NF-YA/B/C. We have characterized NF-Y of the trematode parasite Schistosoma mansoni and studied the structure and the function of the SMNF-YA subunit. In this work, we present the cloning and sequence analysis of the B subunit of the parasite factor. SMNF-YB contains the conserved HAP-3 homology domain but the remaining part of the protein was found to be highly divergent from all other species. We demonstrated by transfections of GAL4 fusion constructs, that mouse NF-YB does not contain activation domains while the C-terminal part of SMNF-YB has transcriptional activation potential. On the other hand, the N-terminal parts of SMNF-YA and mouse NF-YA were shown to mediate transactivation; the integrity of a large 160 amino acid glutamine-rich domain of NF-YA was required for this function and an adjacent serine- and threonine-rich domain was necessary for full activity in HepG2, but redundant in other cell types. Transactivation domains identified in SMNF-YB are also rich in serine and threonine residues. Our results indicate that serine/threonine-richsequences from helminth parasites potentiate trans-cription and that such structures have diverged during evolution within the same transcription factor.

NF-Y organizes the gamma-globin CCAAT boxes region

The CCAAT-binding activator NF-Y is formed by three evolutionary conserved subunits, two of which contain putative histone-like domains. We investigated NF-Y binding to all CCAAT boxes of globin promoters in direct binding, competition, and supershift electrophoretic mobility shift assay; we found that the alpha, zeta, and proximal gamma CCAAT boxes of human and the prosimian Galago bind avidly, and distal gamma CCAAT boxes have intermediate affinity, whereas the epsilon and beta sequences bind NF-Y very poorly. We developed an efficient in vitro transcription system from erythroid K562 cells and established that both the distal and the proximal CCAAT boxes are important for optimal gamma-globin promoter activity. Surprisingly, NF-Y binding to a mutated distal CCAAT box (a C to T at position -114) is remarkably increased upon occupancy of the high affinity proximal element, located 27 base pairs away. Shortening the distance between the two CCAAT boxes progressively prevents simultaneous CCAAT binding, indicating that NF-Y interacts in a mutually exclusive way with CCAAT boxes closer than 24 base pairs apart. A combination of circular permutation and phasing analysis proved that (i) NF-Y-induced angles of the two gamma-globin CCAAT boxes have similar amplitudes; (ii) occupancy of the two CCAAT boxes leads to compensatory distortions; (iii) the two NF-Y bends are spatially oriented with combined twisting angles of about 100 degrees. Interestingly, such distortions are reminiscent of core histone-DNA interactions. We conclude that NF-Y binding imposes a high level of functionally important coordinate organization to the gamma-globin promoter.

Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis

The CCAAT motif is found in the promoters of many eukaryotic genes. In yeast a single complex of three proteins, termed HAP2, HAP3, and HAP5, binds to this sequence, and in mammals the three components of the equivalent complex (called variously NF-Y, CBF, or CP1) are also represented by single genes. Here we report the presence of multiple genes for each of the components of the CCAAT-binding complex, HAP2, 3,5, from Arabidopsis. Three independent Arabidopsis HAP subunit 2 (AtHAP2) cDNAs were cloned by functional complementation of a yeast hap2 mutant, and two independent forms each of AtHAP3 and AtHAP5 cDNAs were detected in the expressed sequence tag database. Additional homologs (two of AtHAP3 and one of AtHAP5) have been identified from available Arabidopsis genomic sequences. Northern-blot analysis indicated ubiquitous expression for each AtHAP2 and AtHAP5 cDNA in a range of tissues, whereas expression of each AtHAP3 cDNA was under developmental and/or environmental regulation. The unexpected presence of multiple forms of each HAP homolog in Arabidopsis, compared with the single genes in yeast and vertebrates, suggests that the HAP2,3,5 complex may play diverse roles in gene transcription in higher plants.

The Neurospora aab-1 gene encodes a CCAAT binding protein homologous to yeast HAP5

The expression of the am (glutamate dehydrogenase) gene is dependent upon two upstream activating sequences, designated URSam(alpha) and URSam(beta). A heteromeric nuclear protein Am Alpha Binding protein (AAB) binds specifically to a CCAAT box within the URSam(alpha) element. AAB appears to be composed of three components. We used polyclonal antiserum raised against the highly purified AAB1 subunit to isolate a partial aab-1 cDNA clone, which was then used to isolate a full-length cDNA and a genomic clone. The full-length cDNA has the potential to encode a 272 amino acid protein with a calculated molecular weight of 30 kD. Amino acid sequence obtained by Edman analysis of the AAB1 protein confirmed that the aab-1 gene had been cloned. AAB-1 shows similarity to the HAP5 protein of yeast and the CBF-C protein of rat. Each of these proteins is an essential subunit of their respective heteromeric CCAAT binding proteins. The aab1 gene maps on linkage group III of Neurospora crassa near the trp-1 locus. Disruption of the aab-1 gene results in pleiotropic effects on growth and development as well as a 50% reduction in glutamate dehydrogenase levels. Transformation of the aab-1 disruption mutant strain with the cloned genomic copy of the aab-1 gene rescued all of the phenotypic alterations associated with the aab-1 mutation.

Cloning and expression of human NF-YC

The CCAAT box is an important element in eukaryotic promoters and NF-Y (CBF) is a conserved heterotrimeric protein binding to it. Two subunits, NF-YB and NF-YC, contain a histone-like motif. We cloned the complete cDNA coding for the human NF-YC gene. The ORF codes for a 335 aa protein that shows virtual identity to the rat sequence, confirming the stunning invariance of NF-Y genes across species. We expressed and purified the yeast homology domain of NF-YC in bacteria and performed EMSA together with the corresponding conserved domains of NF-YA and NF-YB, obtaining a CCAAT-binding mini-NF-Y. We evaluated the expression of NF-YC and found that mRNA levels are similar in different human tissues except in testis.

Functional analysis of the Schistosoma mansoni 28 kDa glutathione S-transferase gene promoter: involvement of SMNF-Y transcription factor in multimeric complexes

The ability of the 5' flanking region of the gene encoding the 28 kDa glutathione S-transferase of Schistosoma mansoni gene to promote transcription, was studied in different mammalian cell lines. Results of transient transfection assays showed a strong activity of the -277 to +1 nt region of the Sm28GST gene, comparable to that of well-studied promoters. Deletion analysis indicated that an AP-1 site and two closely located CCAAT (Y1 and Y2) boxes were the principal motifs responsible for the promoter activity. Binding of the NF-Y complex to Y1 and Y2, as well as to a third CCAAT box (Y3) close to the promoter TATA box, was compared in gel shift and super-shift experiments. All of the three Y boxes bound protein complexes from S. mansoni nuclear extracts that were shown to contain the A subunit of the schistosome NF-Y complex (SMNF-YA). Competition assays revealed a differential affinity of the Y1, Y2 and Y3 sequences for NF-Y. The Y1, Y2 and Y3 regions were also shown to activate transcription when included in an heterologous promoter and data obtained strongly suggested the involvement of SMNF-Y in multimeric complexes during this process.

The sequence of 55 kb on the left arm of yeast chromosome XVI identifies a small nuclear RNA, a new putative protein kinase and two new putative regulators

We have sequenced and analysed a 55786 bp fragment located on the left arm of chromosome XVI of Saccharomyces cerevisiae. The sequence contains 29 non-overlapping open reading frames (ORFs) longer than 300 bp, among which 12 genes have previously been sequenced: OYE3, REV3, SVS1, BEM4, CDC60, KIP2, PEP4, SPK1, PAL1, KES1, SNR17B and RPL37A. Three new ORFs, P2591, P2594 and P2597 are highly homologous to the human phosphotyrosyl phosphatase activator PTPA, to the pleiotropic regulator PRL1 of PP1 and PP2a protein phosphatases in plants and to the protein kinase PAR-1 in Caenorhabditis elegans, respectively. Three other ORFs, P2545, P2567 and P2578 have significant homology with ORFs of unknown function located on yeast chromosomes VIII, XVI and IV respectively.

Interactions of the yeast centromere and promoter factor, Cpf1p, with the cytochrome c1 upstream region and functional implications on regulated gene expression

The upstream activation site (UAS) of the cytochrome c1 gene, CYT1, contains sequences for DNA-binding of several transcription factors. Among them are the heme-dependent protein, Hap1p, and the multiprotein complex, Hap2/3/4/5, which mediate transcriptional induction under aerobic conditions and after exhaustion of glucose, respectively. The multiple interactions of nuclear proteins with the UAS region of CYT1 observed in electrophoretic mobility shift experiments are influenced by carbon source and oxygen tension, but are independent of both regulators, Hap1p and Hap2/3/4/5. All protein-DNA complexes obtained are solely due to the association of the centromere and promoter factor 1 (Cpf1p) with the centromere determining element (CDE I)-like motif at the 5' boundary of the UAS(CYT1). This motif overlaps with a consensus sequence for the binding of the general factor Abf1p. Functional analyses after the separate introduction of point mutations into both elements reveal no role for the latter protein and only a minor role for Cpf1p in the regulated expression of CYT1/lacZ chimaeric proteins. However, in cpf1-mutants, induction of CYT1 reaches higher steady state levels and adaptation to aerobic conditions occurs faster than in wild-type. Thus, Cpf1p seems to reduce CYT1 promoter activity under partly inducing conditions, e.g. when only one of the activators, Hap1p or the Hap2 complex, exerts its function.

Cloning of Schistosoma mansoni transcription factor NF-YA subunit: phylogenic conservation of the HAP-2 homology domain

The CCAAT-binding factor NF-Y (CBF/CP1) is a heteromeric transcription factor involved in the regulation of a variety of eukaryotic genes. We identified NF-Y as the CCAAT activity binding to the promoter region of the gene coding for the 28-kDa glutathione S-transferase of the human parasite Schistosoma mansoni (Sm28GST). We isolated the NF-YA cDNA from S. mansoni (SmNF-YA): the complete 268 amino acid sequence harbors a region in its C-terminal part that shows homology with the subunit interaction and DNA-binding domains of the mammalian NF-YA; the N-terminal region has an amino acid composition reminiscent of the mammalian and echinoderm counterparts, rich in glutamine and hydrophobic residues, but shows no sequence similarity at the primary level. In vitro synthesized SMNF-YA is able to associate with mammalian NF-YB/C subunits in the absence of DNA and to bind to the Sm28GST CCAAT box. Surprisingly, a monoclonal antibody directed against the non-conserved Q-rich activation domain of mammalian NF-YA supershifts and immunoprecipitates SMNF-YA, strongly suggesting structure conservation in the activation domain between divergent species.

The response regulator-like protein Pos9/Skn7 of Saccharomyces cerevisiae is involved in oxidative stress resistance

We have isolated mutants of Saccharomyces cerevisiae with an increased sensitivity to oxidative stress. All pos9 mutants (pos for peroxide sensitivity) were hypersensitive to methylviologene, hyperbaric oxygen or hydrogen peroxide, but grew similarly to the wild-type under all other conditions tested. Isolation and sequencing of the respective POS9 gene revealed that it was identical to SKN7. The predicted Skn7/Pos9 protein possesses a domain with high homology to prokaryotic response regulators. These regulatory proteins are part of a simple signalling cascade termed a "two-component system", where a phosphorylation signal of a histidine kinase is transferred to a conserved aspartate residue of the response regulator. To test the functional role of the respective aspartate residue of Skn7/Pos9 protein in oxidative stress, we mutagenized this residue in vitro to alanine, arginine and glutamate. Only the glutamate allele (D427 to E) was able to rescue the hydrogen peroxide-sensitivity of pos9 mutants. By fusion experiments with the Gal4 DNA-binding domain we identified the isolated response regulator-like domain as a novel eukaryotic domain sufficient for gene activation. Whereas this hybrid protein activated transcription of a lacZ reporter gene under aerobic conditions, no activation was observed under anaerobic conditions, indicating that the response regulator domain is involved in a signalling reaction. Two-hybrid investigations also suggest an oligomerization of the Pos9 protein. Our results indicate that a two-component system is involved in the oxidative-stress response of yeast.

Cloning and characterization of a Brassica napus gene encoding a homologue of the B subunit of a heteromeric CCAAT-binding factor

The CCAAT motif present in the promoter of several genes is recognized in yeast and animals by a highly specific heteromeric factor (variously called HAP, CBF, CP1 or NF-Y) which is composed of a minimum of three subunits. A plant homologue of the CBF-B/HAP2 subunit is described for the first time in this report. Sequence comparison of the Brassica napus (Bn) CCAAT-binding factor (CBF) B subunit with the homologous yeast and animal proteins revealed that the critical amino-acid domains involved in DNA binding and subunit assembly are also conserved in plants. Interestingly, the Gln-rich regions found in the animal and yeast proteins, which may be involved in transcriptional activation, are absent in the Bn CBF-B subunit. The analysis of various cDNAs and of a genomic clone revealed the presence of alternatively spliced transcripts which could originate from different promoters.

Regulation of mitochondrial biogenesis in Saccharomyces cerevisiae. Intricate interplay between general and specific transcription factors in the promoter of the QCR8 gene

Transcription of the QCR8 gene, encoding subunit VIII of the Saccharomyces cerevisiae mitochondrial ubiquinol-cytochrome c oxidoreductase (QCR), is controlled by the carbon-source-dependent heme-activator protein complex HAP2/3/4 and the general transcriptional regulators autonomous replication-site-binding factor ABF1 and centromere-binding and promoter-binding factor CPF1. In this study, we investigate and dissect the relative contributions and mutual interactions of these regulators in transcriptional control. Transcription was analyzed both under steady-state conditions and during nutritional shifts, in hap delta mutants and after site-specific mutagenesis of the various binding sites in the chromosomal context of the QCR8 gene. We present evidence for both direct and indirect interactions between ABF1 and HAP2/3/4, and show that HAP2/3/4 is essential for a rapid transcriptional induction during transition from repressed to derepressed conditions. However, the activator is not the only determinant for carbon-source-dependent regulation, and we observe a functional difference between HAP2/3/4 and the HAP2/3 subcomplex. ABF1 is required for maintainance of basal repressed and derepressed transcription in the steady state of growth. The repressive action of the negative modulator CPF1 during escape from glucose repression is overcome through the cooperative action of ABF1 and HAP2/3/4. The implications of the intricate interactions of these DNA-binding regulators for control of expression of mitochondrial protein genes are discussed.

Sequencing analysis of a 15.4 kb fragment of yeast chromosome XIV identifies the RPD3, PAS8 and KRE1 loci, five new open reading frames

The DNA sequence of a 15.4 kb region covering the left arm of chromosome XIV from Saccharomyces cerevisiae was determined. This region contains eight open reading frames (ORFs) which code for proteins of more than 100 amino acids. Three ORFs correspond to the RPD3, PAS8 and KRE1 loci, described previously. Three ORFs show limited homology with known proteins: NO330 with the recessive suppressor of secretory defect SAC1, NO325 with YCR094W identified during chromosome III sequencing; whereas NO315 presents a motif conserved in the dnaJ family. Two ORFs (NO320 and NO325) show no homology to known proteins within the databases screened, but NO320 corresponds to a serine-threonine-rich protein. The sequence has been entered in the EMBL data library under Accession Number Z46259.

The respiratory system of Kluyveromyces lactis escapes from HAP2 control

A functional homolog of the Saccharomyces cerevisiae HAP2 gene, coding for one element of a transcriptional activator complex, was cloned from the yeast Kluyveromyces lactis and its nucleotide sequence was determined. Inactivation of the gene had no significant effect on respiration-dependent growth, suggesting that the HAP2/3/4 complex has no major control over the formation of the mitochondrial respiratory system in K. lactis.

The sequence of a 36 kb segment on the left arm of yeast chromosome X identifies 24 open reading frames including NUC1, PRP21 (SPP91), CDC6, CRY2, the gene for S24, a homologue to the aconitase gene ACO1 and two homologues to chromosome III genes

A 36 kb fragment from the left arm of chromosome X, located at about 50 kb from the telomere, was sequenced and analysed. The segment contains a new putative ARS, a new tRNA for threonine, remnants of a solo delta and 24 open reading frames (ORFs) numbered from J0310 to J0355. Six of them, NUC1, PRP21 (also called SPP91), CDC6, CRY2, the gene encoding the ribosomal protein S24 and the gene coding for a hypothetical protein of 599 amino acids, have been sequenced previously. Three ORFs show high homology to the yeast gene ACO1 encoding mitochondrial aconitase and to the chromosome III genes YCR34W and YCR37C of unknown function. Three other ORFs show lower but significant homology: a first one to UNP, a gene related to the tre-2 oncogene from mouse and to the gene coding for the yeast deubiquitinating enzyme DOA2; a second one to SLY41, a suppressor of the functional loss of YPT1 and a third one to the gene encoding the proline utilization activator PUT3.

MBR1 and MBR3, two related yeast genes that can suppress the growth defect of hap2, hap3 and hap4 mutants

Two new yeast genes, named MBR1 and MBR3, were isolated as multicopy suppressors of the growth defect of a strain lacking the HAP2 transcriptional activator. Both genes when overexpressed can also suppress the growth defect of hap3 and hap4 null mutants. However, overexpression of MBR1 cannot substitute for the HAP2/3/4 complex in activation of the CYC1 gene. Nucleotide sequencing of MBR1 and MBR3 revealed that these two genes encode serine-rich, hydrophilic proteins with regions of significant homology. The functional importance of one of these conserved regions was shown by mutagenesis. Disruption of MBR1 leads to a partial growth defect on glycerol medium. Disruption of MBR3 has no major effect but the double disruptant shows a synthetic phenotype suggesting that the MBR1 and MBR3 gene products participate in common function.

Expression of the Saccharomyces cerevisiae CYT2 gene, encoding cytochrome c1 heme lyase

In this paper we examine the expression of the Saccharomyces cerevisiae CYT2 gene, which encodes cytochrome c1 heme lyase. This enzyme is required for covalent attachment of heme to apocytochrome c1, a subunit of the mitochondrial respiratory chain. Transcription of the 1-kb CYT2 mRNA initiates at four prominent sites at a distance of 52-225 bp in front of the AUG start codon. The level of CYT2 mRNA is not influenced by the presence or absence of oxygen or of heme, but it is subject to carbon-source control. The concentration of the CYT2 mRNA is significantly reduced in glucose-grown cells as compared to cells grown under non-repressing conditions. Neither the HAPp activator proteins nor MIG1p, a repressor protein involved in glucose repression, seem to mediate this effect.

Studies on the structure of the mouse CBF-A gene and properties of a truncated CBF-A isoform generated from an alternatively spliced RNA

CCAAT-binding factor (CBF), a heteromeric transcription factor that binds to sequences containing a CCAAT motif, is composed of three subunits, A, B and C, which are all required for DNA binding. The mouse CBF-A gene contains seven coding exons, which span 12 kb. Evidence is also presented for an additional 5' untranslated exon. The 90-amino-acid (aa) segment of CBF-A, which shows a high degree of sequence identity with the yeast transcription factor, HAP3, is split into exons 3 and 4. An alternatively spliced RNA that lacks exon 3 was identified by polymerase chain reaction. Although removal of exon 3 interrupts the CBF-A reading frame, a potential start codon at the 3' end of exon 2 is in the same reading frame as the reading frame encoding CBF-A in exons 4 to 7. A CBF-A polypeptide of the predicted 17-kDa, size, was indeed identified after in vitro transcription and translation of the DNA complementary to RNA (cDNA) corresponding to the alternatively spliced CBF-A mRNA. In contrast to full-length CBF-A, this truncated CBFA did not bind to a DNA sequence containing the CCAAT motif in the presence of the other two components of CBF. This result indicates that the segment corresponding to the exons missing in the truncated isoform of CBF-A is essential for the binding of CBF to DNA.

Expression of yeast cytochrome c1 is controlled at the transcriptional level by glucose, oxygen and haem

The nuclear gene for cytochrome c1 in Saccharomyces cerevisiae (CYT1) was localized on chromosome XV. Its upstream region was identified by functional complementation. Fusion to the lacZ reporter gene on a CEN plasmid allowed study of the effect of carbon sources and of specific deletion mutations on expression of the gene in yeast transformants. Detailed promoter analysis combined with expression studies in recipient strains defective in regulatory genes identified cis-acting sites and transcription factors involved in the regulated expression of the cytochrome c1 gene. These analyses showed that, in the presence of glucose, transcription of CYT1 is positively controlled by oxygen, presumably through the haem signal, and mediated by the HAP1-encoded transactivator. It is additionally regulated by the HAP2/3/4 complex which mediates gene activation mainly under glucose-free conditions. Basal transcription is, in part, effected by CPF1, a centromere and promoter-binding factor.

Identification of nuclear genes which participate to mitochondrial translation in Saccharomyces cerevisiae

The mitochondrial protein synthesis presents specific features and uses specific components different from their cytoplasmic counterparts. Since most genes which code for these components are localized in the chromosomes and only a small number are encoded by the mitochondrial DNA, it is important to identify and characterize the nuclear genes involved in this process. In order to do this, we have used a genetic screening which implies the selection and study of nuclear suppressors of mitochondrial mutations (or the reverse situation) which affect the mitochondrial protein synthesis. Three mutations have been used for this purpose. Two of them (ts 1398, cs 909) impair the mitochondrial ribosome; they were used to characterize new interacting components as well as two genes, MBR1 and MBR2, which control the assembly or the regulation of other genes involved in mitochondrial protein synthesis. The third mutation (ts 932), blocks the 3'-end maturation of the mitochondrial aspartyl tRNA. A nuclear suppressor has been obtained which presents all the characteristics of a mutation in the gene encoding the enzyme responsible for this process.

Characterization of Hex2 protein, a negative regulatory element necessary for glucose repression in yeast

The regulatory HEX2 gene plays an important role in glucose repression in the yeast Saccharomyces cerevisiae. The hex2 mutants have pleiotropic defects in the regulation of glucose-repressible enzymes, hexokinase PII synthesis and maltose uptake [Entian, K.-D. & Zimmermann, F.K. (1980) Mol. Gen. Genet. 177, 345-350]. The HEX2 gene encodes a protein of 114137 Da, deduced from its DNA sequence. There were no strong similarities to previously known genes. HEX2-lacZ fusions revealed a largely constitutive expression when repressing and non-repressing growth conditions were compared. Cellular fractionation studies indicated a nuclear localization of the Hex2 protein. The hex2 mutation was shown to be allelic to reg1, which releases galactose pathway enzymes from glucose repression [Matsumoto, K., Yoshimatsu, T. & Oshima, Y. (1983) J. Bacteriol. 153, 1405-1414]. Overexpression of HEX2 resulted in a 70% reduction of GAL1 expression under induced growth conditions. Our studies support the view that protein Hex2 is a negative regulatory element in glucose repression which may directly influence transcription, possibly by interaction with transcriptional factors. Deletion experiments identified a central core of Hex2, spanning only 492 out of 1026 amino acid residues, as mainly important for glucose repression. There are two strongly acidic regions within this part of the protein, their possible importance is discussed.

The GAM1/SNF2 gene of Saccharomyces cerevisiae encodes a highly charged nuclear protein required for transcription of the STA1 gene

We have cloned and sequenced the GAM1 gene which is required for transcription of the STA1 gene encoding an extracellular glucoamylase in Saccharomyces cerevisiae var. diastaticus. Complementation tests indicated that GAM1 is the same gene as SNF2 which is required for derepression of the SUC2 gene encoding invertase. Accumulation of SNF2 RNA was not regulated by the GAM2 and GAM3 genes which are also required for STA1 expression. The SNF2 gene was predicted to encode a 194 kDa highly charged protein with a glutamine-rich tract. A bifunctional SNF2-lacZ fusion protein was shown by immunofluorescence microscopy to be localized to the nucleus, suggesting that the SNF2 protein is located in the nucleus.

A yeast protein with homology to the beta-subunit of G proteins is involved in control of heme-regulated and catabolite-repressed genes

The product of the Saccharomyces cerevisiae AER2 gene is responsible for maintaining repression of at least two distinct regulatory pathways: heme activation/repression and catabolite repression. Mutations in the gene caused an eightfold increase in the expression of the heme-activated CYC1 gene in the absence of heme, a substantial increase in the expression of the heme-repressed ANB1 gene in the presence of heme, and a 13-fold increase in the expression of the catabolite-repressed GAL1 gene in the presence of glucose. Lesser or no increases in the expression of these genes were observed under derepressed or activation conditions. The aer2 mutations also caused a large increase in CYC7 gene expression under all conditions; this gene is subject to heme activation/repression, as well as catabolite repression. The AER2 gene was cloned and the sequence determined. The large open reading frame contiguous with the transcript from the complementing region encoded a 713-amino acid polypeptide chain with extensive homology to the beta-subunit of G proteins. The sequence revealed that AER2 is the TUP1 gene. A deletion mutation was constructed and the null phenotype was the same as the original mutants. The aer2 null mutant was shown to have increased aerobic and anaerobic levels of RNA encoding the ROX1 repressor, normally expressed only aerobically and responsible for the aerobic repression of ANB1 expression. The increase in both ROX1 and ANB1 RNAs aerobically in this mutant suggests that the repressor is nonfunctional in the mutant.