A single Saccharomyces cerevisiae upstream activation site (UAS1) has two distinct regions essential for its activity

MOLECULAR DYNAMICS STUDY OF THE TRANSCRIPTIONAL RECOGNITION MECHANISM OF HEME ACTIVATE PROTEIN (HAP)

The heme activate protein (HAP) is a model system for understanding protein–DNA interactions and allosteric mechanisms in gene regulation. Despite the wealth of biochemical data provided by extensive mutations of HAP, the specific recognition mechanism of the target DNA by HAP has remained elusive. This paper gives the results of a study using molecular dynamics simulations performed for a single DNA fragment (USACYC7) and three protein–DNACYC7complex crystal structures: the HAP-wt and two HAP mutants — HAP-PC7: S63G; HAP-18: S63R. Comparative molecular dynamics simulations reveal that the distributions of protein–DNA interactions recognizing the key base steps (CGC) are consistent with their transcriptional activities. Relative to the similar conformations of three bound DNA, the different flexibilities in involving DNA recognition regions: N-term Arm and Zn 2 Cys 6 Binuclear Cluster in three HAPs may result in a variety of protein–DNA recognitions. Despite different intensities of motions, the essential dynamics (ED) analysis shows that the internal motions of three protein–DNA complexes are similar: three proteins all slide along DNA to find their target sites. Thus, under this condition, during the recognition process, the flexibility of the DNA recognizing regions (N-term Arm and Zn 2 Cys 6 Binuclear Cluster regions) plays a crucial role in determining the abilities of protein's recognizing DNA: the higher is its flexibility, the faster it slides along the DNA to find the targeted DNA.

Expression of recombinant cytochromes c from various species in Saccharomyces cerevisiae: post-translational modifications

A complete protocol for the expression of recombinant cytochrome c genes from yeast, Drosophila melanogaster, and rat in a yeast strain, GM-3C-2, which does not express its own cytochromes c is described. The construction of the expression vectors, transformation and large-scale growth of the yeast, and preparation and purification of the recombinant cytochromes c are described. It was found that, contrary to the way yeast modifies its own cytochromes c, the recombinant proteins were partially acetylated at their N-terminus, except for the drosophila protein, which remained entirely unblocked. Furthermore, the yeast and rat proteins were close to fully trimethylated at lysine 72, while the drosophila protein could be separated chromatographically into forms containing tri-, di-, mono-, and unmethylated lysine 72 showing corresponding resonances in the NMR spectrum. These observations emphasize that, in employing expression procedures to obtain native or mutant forms of cytochrome c, it is essential to identify the variety and extent of post-translational modifications and to separate the preparation into pure monomolecular species. Otherwise, it may become impossible to distinguish between the influence of a site-directed mutation and unexamined post-translational modifications.

Characterization of the cytochrome c gene from the starch-fermenting yeast Schwanniomyces occidentalis and its expression in Baker's yeast

A cytochrome c protein gene, CYC10, of the dextran- and starch-fermenting yeast, Schwanniomyces occidentalis was cloned and characterized. The DNA sequence was determined, and the predicted amino acid sequence of the protein-coding region shares close homologies to the cytochrome c genes. A S. occidentalis strain with a disruption of the gene revealed that CYC10 was the only functional cytochrome c protein-encoding gene in S. occidentalis, unlike the two cytochrome c protein genes (CYC1 and CYC7) in Saccharomyces cerevisiae. The CYC10 gene was oxygen-induced but not subject to catabolite repression. The expression of the CYC10 gene was studied in the heterologous yeast S. cerevisiae. The oxygen induction of the gene was found to be identical to that of the CYC1 gene, indicating that these two genes share similar or closely related cis- and trans-acting oxygen regulatory elements. However, the CYC10 gene was glucose repressed in S. cerevisiae strains; a phenomenon which was not observed in the native S. occidentalis cells. Search in the 5' untranslated region of the CYC10 gene revealed some homologies at -425 to -405 to UAS1 of the S. cerevisiae CYC1 gene. A deletion of a segment of upstream region including this sequence abolished expression in S. cerevisiae. Finally the phylogenetic relationships of different yeasts and fungi were determined based upon the amino acid sequences of the cytochrome c proteins. These relationships do not completely agree with classical divisions.

Regulation of sugar and ethanol metabolism in Saccharomyces cerevisiae

This review briefly surveys the literature on the nature, regulation, genetics, and molecular biology of the major energy-yielding pathways in yeasts, with emphasis on Saccharomyces cerevisiae. While sugar metabolism has received the lion's share of attention from workers in this field because of its bearing on the production of ethanol and other metabolites, more attention is now being paid to ethanol metabolism and the regulation of aerobic metabolism by fermentable and nonfermentable substrates. The utility of yeast as a highly manipulable organism and the discovery that yeast metabolic pathways are subject to the same types of control as those of higher cells open up many opportunities in such diverse areas as molecular evolution and cancer research.

Functional dissection and sequence of yeast HAP1 activator

We present the DNA sequence and a functional dissection of the 1483 residue yeast activator HAP1. Salient results are, first, a single DNA binding domain (1-148) specifies binding to the two target sites of different sequence, UAS1 and CYC7. This domain contains a cysteine-rich zinc finger, and mutation of either of two cysteines abolishes binding to both sites. Second, mutations that specifically abolish binding to UAS1 or to CYC7 exist. These changes lie either in the residue immediately amino-terminal to the finger or in sequences carboxyl to the finger. Thus, both the base of the finger and carboxyl flanking residues are involved in specific DNA binding. Third, a distinct region (residues 245-445) mediates heme induction by masking the DNA binding domain in the absence of inducer; heme counteracts this masking, perhaps by interacting with a repeat sequence of metal binding character in this region. While sequences between 445 and 1308 have no obvious function, a highly acidic carboxyl terminus mediates transcriptional activation by HAP1.

DNA-bound Fos proteins activate transcription in yeast

We constructed genes encoding the DNA binding region of the bacterial LexA repressor fused to the v-fos and c-fos oncogene products. The resulting LexA-Fos fusion proteins activated transcription in yeast. Transcription activation by these proteins was as strong as transcription activation by proteins native to yeast. LexA-Fos fusion proteins only activated transcription of genes when they were bound to LexA binding sites inserted upstream of those genes. Transcription was activated less strongly by similar proteins in which the DNA binding region of LexA was fused to vMyc and cMyc. Transcription was not activated by native LexA or by proteins containing the DNA binding domain of LexA fused to bacteriophage 434 repressor or yeast MAT alpha 2 protein. These results demonstrate that Fos proteins activate eukaryotic gene expression when they are bound to promoter DNA, and thus suggest that Fos proteins exert some of their effects because they stimulate transcription of cellular genes. Regulation of transcription by Fos and Myc proteins in yeast provides a phenotype that may facilitate genetic analysis of the function of these proteins in higher organisms.

Yeast HAP1 activator binds to two upstream activation sites of different sequence

We show that the HAP1 protein binds in vitro to the upstream activation site (UAS) of the yeast CYC7 gene. Strikingly, this sequence bears no obvious similarity to the sequence bound by HAP1 at UAS1 of the CYC1 gene. The CYC1 and CYC7 sites compete for binding to HAP1 and have comparable affinities for the protein. The gross features of the interaction of HAP1 with the two sites are similar: multiple major and minor groove contacts, spanning 23 bp, on one helical face, with a back-side major groove contact toward one end. The precise positions of the contacts differ, however. A mutant form of HAP1, HAP1-18, abolishes the ability of the protein to bind to UAS1 but not CYC7 DNA. Possible mechanisms for how a single protein recognizes two sequences are discussed.

Yeast HAP1 activator competes with the factor RC2 for binding to the upstream activation site UAS1 of the CYC1 gene

We show that the yeast HAP1 activator locus encodes a protein that binds in vitro to the upstream activation site, UAS1, of the CYC1 gene (iso-1-cytochrome c). Binding of wild-type HAP1 and truncated HAP1 derivatives to UAS1 is evident in crudely fractionated yeast extracts using the gel electrophoresis DNA binding assay. The binding of HAP1 in vitro, like the activity of UAS1 in vivo, is stimulated by heme. HAP1 binds to region B, one of two portions of UAS1 shown to be important by genetic analysis of the site. Surprisingly, HAP1 binds to the same sequence as a second factor, RC2. Both HAP1 and RC2 bind to the same side of the helix, and make similar but not identical major and minor groove contacts that span two full turns. An additional factor that binds to the second important part of UAS1, the region A factor (RAF), is also identified. A model depicting the interplay of HAP1, RC2, and RAF in the control of UAS1 is presented.