Specific cis-acting sequence for PHO8 expression interacts with PHO4 protein, a positive regulatory factor, in Saccharomyces cerevisiae

Engineering and optimization of phosphate-responsive phytase expression in Pichia pastoris yeast for phytate hydrolysis

Phytate is the major storage form of phosphorus in plants. It is present in cereals and raw materials of vegetable origin used in animal and human diets. However, non-ruminant animals have little phytase activity in their guts and, therefore, cannot digest phytate. As a result, almost all dietary phytate is discharged into the environment, causing phosphorus pollution. Phytate is also considered as an "antinutrient" for its ability to form insoluble and stable complexes with metal ions, thus reducing dietary absorption of essential minerals. It is a dire need to develop sustainable approaches for environmentally-friendly utilization for this valuable and abundant natural resource. To this end, we engineered Pichia pastoris to express and secrete phytase in a "made-to-order" fashion in response to external level of inorganic phosphate (Pi). Responsiveness to external Pi level was achieved by generating a Pi-responsive promoter library using directed evolution. The resultant yeast strains were proven to liberate Pi from wheat-based meal in a simulated in vitro digestion model. These yeast-based whole cell biocatalysts may serve as platform hosts with potential applications in food processing industry and animal waste treatment.

Isolation and characterization of a sodium-dependent phosphate transporter gene in Dunaliella viridis

A sodium-dependent phosphate transporter gene, DvSPT1, was isolated from a cDNA library using a probe derived from a subtracted cDNA library of Dunaliella viridis. Sequencing analyses revealed a cDNA sequence of 2649 bp long and encoded an open-reading frame consisting of 672 amino acids. The deduced amino acid sequence of DvSPT1 exhibited 31.2% identity to that of TcPHO from Tetraselmis chui. Hydrophobicity and secondary structure prediction revealed 11 conserved transmembrane domains similar to those found in PHO89 from Saccharomyces cerevisiae and PHO4 from Neurospora crassa. Northern blot analysis indicated that the DvSPT1 expression was induced upon NaCl hyperosmotic stress or phosphate depletion. Functional characterization in yeast Na+ export pump mutant G19 suggested that DvSPT1 encoded a Na+ transporter protein. The gene sequence of GDvSPT1 (7922 bp) was isolated from a genomic library of D. viridis. Southern blot analysis indicated that there exist at least two homologous genes in D. viridis.

A model for the complex between the hypoxia-inducible factor-1 (HIF-1) and its consensus DNA sequence

Hypoxia-inducible factor-1 (HIF-1) is a heterodimeric transcription factor activated by hypoxia. When activated, HIF-1 mediates the differential expression of genes such as erythropoietin and Vascular Endothelial Growth Factor (VEGF) during hypoxia. It is composed of two different subunits, HIF-1alpha and ARNT (Aryl Receptor Nuclear Translocator). These two subunits belong to the bHLH (basic Helix-Loop-Helix) PAS (Per, Ahr/ARNT, Sim) family. The bHLH domain of these factors is responsible for dimerization through the two helices and for DNA binding through their basic domain. In this work, we used various methods of molecular modeling in order to develop a 3D structure for the HIF-1 bHLH domain bound to its DNA consensus sequence. Firstly, the 3D structure of the bHLH domain of both subunits based on their amino acid sequence was defined. Secondly, we compared this model with data from known crystal structures of basic leucine zipper-DNA and bHLH-DNA complexes in order to determine a potential canvas for HIF-1. Thirdly, we performed a manual approach of the HIF-1 bHLH domain onto the DNA recognition site using this canvas. Finally, the protein-DNA complex 3D structure was optimized using a Monte Carlo program called MONTY. The model predicted a pattern of interactions between amino acids and DNA bases which reflect for ARNT what is experimentally observed among different X-ray structures of other bHLH transcription factors possessing the H (His), E (Glu), R (Arg) triad, as ARNT does. On the other hand, only the Arg residue is conserved in HIF- 1alpha. We propose from this model that a serine replaces the histidine while an alanine and a lysine also make contacts with DNA. From these results, we postulate that the specificity of HIF-1 toward its DNA sequence could be driven by the HIF-1alpha subunit. The predicted model will be verified by X-Ray currently ongoing.

Transcriptional regulation of the yeast PHO8 promoter in comparison to the coregulated PHO5 promoter

Expression of the PHO8 and PHO5 genes that encode a nonspecific alkaline and acid phosphatase, respectively, is regulated in response to the P(i) concentration in the medium by the same transcription factors. Upon induction by phosphate starvation, both promoters undergo characteristic chromatin remodeling, yet the extent of remodeling at the PHO8 promoter is significantly lower than at PHO5. Despite the coordinate regulation of the two promoters, the PHO8 promoter is almost 10 times weaker than PHO5. Here we show that of two Pho4 binding sites that had been previously mapped at the PHO8 promoter in vitro, only the high affinity one, UASp2, is functional in vivo. Activation of the PHO8 promoter is partially Pho2-dependent. However, unlike at PHO5, Pho4 can bind strongly to its binding site in the absence of Pho2 and remodel chromatin in a Pho2-independent manner. Replacement of the inactive UASp1 element by the UASp1 element from the PHO5 promoter results in more extensive chromatin remodeling and a concomitant 2-fold increase in promoter activity. In contrast, replacement of the high affinity UASp2 site with the corresponding site from PHO5 precludes chromatin remodeling completely and as a consequence promoter activation, despite efficient binding of Pho4 to this site. Deletion of the promoter region normally covered by nucleosomes -3 and -2 results in a 2-fold increase in promoter activity, further supporting a repressive role of these nucleosomes. These data show that there can be strong binding of Pho4 to a UAS element without any chromatin remodeling and promoter activation. The close correlation between promoter activity and the extent of chromatin disruption strongly suggests that the low level of PHO8 induction in comparison with PHO5 is partly due to the inability of Pho4 to achieve complete chromatin remodeling at this promoter.

The phosphatase system in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae has at least six species of acid and alkaline phosphatases with different cellular localizations, as well as inorganic phosphate (Pi) transporters. Most of the genes encoding these enzymes are coordinately repressed and derepressed depending on the Pi concentration in the growth medium. The Pi signals are conveyed to these genes through a regulatory circuit consisting of a set of positive and negative regulatory proteins. This phosphatase system is interested as one of the best systems for studying gene regulation in S. cerevisiae due to the simplicity of phenotype determination in genetic analysis. With this methodological advantage, considerable amounts of genetic and molecular evidence in phosphatase regulation have been accumulated in the past twenty-five years. This article summarizes the current progress of research into this subject.

The homeodomain protein Pho2p binds at an A/T-rich segment flanking the binding site of the basic-helix-loop-helix protein Pho4p in the yeast PHO promoters

Transcription of the genomic PHO5, PHO81 and PHO84 genes of the PHO regulon requires Pho4p and Pho2p activity, whereas transcription of PHO8 is directed by Pho4p alone. Pho4p binds to two 9-bp motifs, 5'-GCACGTGGG-3' (type 1. e.g. UASp2 of PHO5 and site D of PHO84) and 5'-GCACGTTTT-3' (type 2, e.g. UASp1 of PHO5 and site E of PHO84) in the PHO promoter. Experiments were performed to evaluate the ability of these 9-bp motifs to function as upstream activation sites (UASs) by insertion of various 36-bp fragments bearing the 9-bp motif in a CYC1-lacZ fusion gene. No expression of the lacZ gene was detected with the 36-bp fragment bearing UASp2 of PHO5, whereas similar 36-bp fragments bearing UASp1 of PHO5 and sites D and E of PHO84 showed UAS activity in response to Pi concentration in the medium and to the pho2 mutation. The Pho2p-responsive UASs are flanked by one or two copies of an A/T-rich segment, whereas UASp2 is not. Gel retardation and competition experiments performed using a T7-Pho2p-His chimeric protein showed that Pho2p binds to the 36-bp fragments bearing A/T-rich segment(s) but not appreciably to the 36-bp fragments not bearing such segment(s). Thus, the A/T segments flanking the PHO UASs are Pho2p binding sites and play an important role in PHO regulation.

Regulation of phosphatase synthesis in Saccharomyces cerevisiae--a review

Transcription of the genes encoding acid and alkaline phosphatases and the inorganic phosphate (Pi) transporter of Saccharomyces cerevisiae are coordinately repressed and derepressed depending on the Pi concentration in the culture medium. This phosphatase system is particularly suited for the study of regulatory mechanisms, because the acid phosphatase activity of each colony on a plate is easily detected by specific staining methods and there is a 500-fold difference between the repressed and derepressed levels of acid phosphatase activity. With these advantages, considerable amounts of genetic and molecular evidence have been accumulated in the past two decades. This article summarizes our current knowledge on this subject.

Negative transcriptional regulation of PH081 expression in Saccharomyces cerevisiae

The PH081 gene product functions as an inhibitor of the cyclin-cyclin-dependent kinase pair, Pho80-Pho85, and is required for derepression of acid phosphatase-encoding gene (PH05) expression. PH081 is the only known regulator of this system whose transcriptional expression is regulated by the level of inorganic phosphate. This effect is mediated by the gene products of the PH04 and PH02 (BAS2, GRF10) genes which act as transcription factors. Fine structural analysis of the PH081 promoter region has revealed the existence of a negative regulatory sequence (NRS). That is, removal of this element causes an approx. 4-fold increase in PH081 expression. The NRS functions in either orientation, but only when located downstream from activation sequences. Interestingly, this element shows significant homology to a sequence present in the promoter of the PH08 gene, encoding a phosphate-repressible alkaline phosphatase. An electrophoretic mobility shift assay (EMSA) using whole-cell extracts and a NRS-containing DNA fragment detects a protein which specifically binds to this element.

Structure and distribution of specific cis-elements for transcriptional regulation of PHO84 in Saccharomyces cerevisiae

Transcription of the PHO84 gene encoding a Pi transporter in Saccharomyces cerevisiae is regulated by the Pi concentration in the medium. The promoter region of PHO84 bears five copies of the motif 5'-CACGT(G/T)-3', a candidate for the upstream activation site (UAS) that binds the transcriptional activator protein of the phosphatase regulon, Pho4p. These motifs are found at nucleotides -880 (site A), -587 (B), -436 (C), -414 (D), and -262 (E) relative to the putative ATG codon of PHO84. The Pho4p binds to all five 6-bp motifs with various affinities. Deletion analysis of the PHO84 promoter using a PHO84-lacZ fusion gene and base substitutions in the 6-bp motif revealed that two copies of the 6-bp motif, either C or D, and E, are necessary and sufficient for full regulation of the PHO84 gene. Results of expression studies with a CYC1-lacZ fusion gene with various 36-bp oligonucleotides including the 30-bp sequences around site D or E, or with modified sequences, inserted in the CYC1 promoter region indicated that the 6-bps motif flanked by a thymine nucleotide at its 5' end is much less effective as a UAS site for Pho4p in vivo than other versions. Thus, the consensus sequences for phosphatase regulation are 5'-GCACGTGGG-3' and 5'-GCACGTTTT-3' which differ from the binding sequences for the Cpflp protein required for transcription of the genes in methionine biosynthesis and for centromere function. However, Pho4p binding in vitro was unaffected by modification of the 5' or 3' flanking sites of the 6-bp motif, while modification inside the 6-bp motif affected it severely. The UAS function of the GCACGTTTT motif with respect to the Pi signal depends on its orientation in the promoter sequence.

Promoter analysis of the PHO81 gene encoding a 134 kDa protein bearing ankyrin repeats in the phosphatase regulon of Saccharomyces cerevisiae

The PHO81 gene encoding one of the regulators of the phosphatase regulon in Saccharomyces cerevisiae was mapped 9.8 centimorgans distal from the ser2 locus on the right arm of chromosome VII. Determination of the nucleotide sequence of cloned PHO81 DNA revealed a 3537 bp open reading frame encoding a 134 kDa protein. This protein has six repeats of a 33-amino acid sequence homologous to the ankyrin repeat and an asparagine-rich region. Transcription of PHO81 is activated by Pho4 protein in cooperation with Pho2 (i.e., Bas2/Grf10) protein under the influence of the inorganic phosphate (Pi) concentration in the medium, through the PHO regulatory system. Major transcription initiation sites of PHO81, determined by primer extension analysis, are at nucleotide positions -66 and -65 relative to the ATG codon. Deletion analysis showed that a 95 bp region from nucleotide position -385 to -291 is essential for response to the Pi signals. Purified Pho4 protein protected a 19 bp region (positions -350 to -332) in the 95 bp fragment from DNase I digestion in vitro and the protected region includes the core sequence 5'-CACGTG-3', which is also observed in other genes of phosphate metabolism.

Nucleosome disruption at the yeast PHO5 promoter upon PHO5 induction occurs in the absence of DNA replication

Activation of the PHO5 gene in S. cerevisiae by phosphate starvation was previously shown to be accompanied by the disappearance of four positioned nucleosomes from the promoter. To investigate the mechanism, we replaced the PHO80 gene, a negative regulator of PHO5, by a temperature-sensitive allele. As a consequence, PHO5 can be activated in the presence of phosphate by a temperature shift from 24 degrees C to 37 degrees C. Under these conditions, the promoter undergoes the same chromatin transition as in phosphate-starved cells. Disruption of the nucleosomes by the temperature shift also occurs when DNA replication is prevented. Nucleosomes re-form when the temperature is shifted from 37 degrees C back to 24 degrees C in nondividing cells. Glucose is required for the disruption of the nucleosomes during the temperature upshift, not for their re-formation during the temperature downshift. These experiments prove that DNA replication is not required for the transition between the nucleosomal and the non-nucleosomal state at the PHO5 promoter.

c-myc oncoprotein function

Genetic alterations of the c-myc locus in various malignancies and the ability of c-myc to transform cultured cells and induce tumors in transgenic animals attest to its central role in many neoplasms. By dissecting the c-Myc protein, a number of critical functional domains of c-Myc have been identified and characterized; these findings suggest a model for c-Myc function and intracellular activity (Fig. 4). c-Myc is synthesized in the cytoplasm and undergoes oligomerization another protein such as Max. Its nuclear localization signal allows c-Myc to be targeted to and retained in the nucleus, where the protein seeks out and binds to specific DNA sites, perhaps facilitated by c-Myc's ability to bind non-specifically to DNA. Once bound to specific DNA sequences, c-Myc then activates or inhibits transcription of a number of target genes, with consequent alterations in cell growth and differentiation. Continued studies of c-Myc and its partner Max should further elucidate the mechanisms by which c-Myc can contribute both to the regulation of normal cell growth and the alteration in that regulation in neoplasia.

Cloning, nucleotide sequence, and regulation of MET14, the gene encoding the APS kinase of Saccharomyces cerevisiae

The MET14 gene of Saccharomyces cerevisiae, encoding APS kinase (ATP:adenylylsulfate-3'-phosphotransferase, EC 2.7.1.25), has been cloned. The nucleotide sequence predicts a protein of 202 amino acids with a molecular mass of 23,060 dalton. Translational fusions of MET14 with the beta-galactosidase gene (lacZ) of Escherichia coli confirmed the results of primer extension and Northern blot analyses indicating that the ca. 0.7 kb mRNA is transcriptionally repressed by the presence of methionine in the growth medium. By primer extension the MET14 transcripts were found to start between positions -25 and -45 upstream of the initiator codon. Located upstream of the MET14 gene is a perfect match (positions -222 to -229) with the previously proposed methionine-specific upstream activating sequence (UASMet). This is the same as the consensus sequence of the Centromere DNA Element I (CDEI) that binds the Centromere Promoter Factor I (CPFI) and of two regulatory elements of the PHO5 gene to which the yeast protein PHO4 binds. The human oncogenic protein c-Myc also has the same recognition sequence. Furthermore, in the 270 bp upstream of the MET14 coding region there are several matches with a methionine-specific upstream negative (URSMet) control element. The significance of these sequences was investigated using different upstream deletion mutations of the MET14 gene which were fused to the lacZ gene of E. coli and chromosomally integrated. We find that the methionine-specific UASMet and one of the URSMet lie in regions necessary for strong activation and weak repression of MET14 transcription, respectively. We propose that both types of control are exerted on MET14.