Dissection of the bifunctional ARGRII protein involved in the regulation of arginine anabolic and catabolic pathways.

ARGRII is a regulatory protein which regulates the arginine anabolic and catabolic pathways in combination with ARGRI and ARGRIII. We have investigated, by deletion analysis and fusion to LexA protein, the different domains of ARGRII protein. In contrast to other yeast regulatory proteins, 92% of ARGRII is necessary for its anabolic repression function and 80% is necessary for its catabolic activator function. We can define three domains in this protein: a putative DNA-binding domain containing a zinc finger motif, a region more involved in the repression activity located around the RNase-like sequence, and a large activation domain.     

Regulation of arginine metabolism in Saccharomyces cerevisiae: expression of the three ARGR regulatory genes and cellular localization of their products

Three regulatory proteins are involved in the control of arginine metabolism in yeast: ARGRI, ARGRII and ARGRIII. The control region and part of the coding sequence of the ARGR genes were fused to the Escherichia coli lacZ gene. These chimeras were used to study the expression of the regulatory genes as well as the cellular compartmentalization of the regulatory products. Our results show that the three ARGR proteins are localized in the nucleus and that their synthesis is not regulated by arginine nor by any of the other ARGR products. However, some data suggest that the ARGRIII protein could control ARGRI activity.     

Characterization of two new genes essential for vegetative growth in Saccharomyces cerevisiae: nucleotide sequence determination and chromosome mapping

Based on nucleotide sequence determination, we have identified two new yeast genes FUN80 and FUN81 located on chromosome XIII. They are both essential for cellular growth but their function is still unknown. FUN80 is closely linked to the ARGRI (or ARG80) gene while FUN81 is located next to the ARGRII (or ARG81) gene. Interestingly, the proteins encoded by these two genes have a long stretch of acidic amino acids within their C-terminal portions.     

Isolation and characterization of the positively acting regulatory gene QUTA from Aspergillus nidulans.

The positively acting regulator gene QUTA from Aspergillus nidulans has been identified and located within a cluster of quinic acid utilisation (QUT) genes isolated within a recombinant phage lambda (lambda Q1). The DNA sequence of the QUTA gene reveals a single uninterrupted reading frame coding for a protein of mw 90.416 Kd. The QUTA protein sequence has a protein motif in the form of a putative "DNA finger" that shows strong homology to other such motifs in the GAL4, PPR1, ARGRII, LAC9 and QA1F regulatory gene products of S. cerevisiae, K. lactis and N. crassa. The data presented confirm the view deduced by genetical analysis that the QUTA gene of A. nidulans encodes a protein capable of interacting with QUT specific DNA sequences.     

Methylation analysis of a plasmid containing a mammalian cell cycle regulatory sequence after transient transfection into the host cell

A hamster genomic sequence containing a cell cycle regulatory sequence derived from a histone H3.2 gene was transfected into K12 hamster fibroblasts in the form of plasmid DNA prepared from dam+ E. coli. Analysis of the plasmid DNA recovered 72 hr after the transfection revealed that it was resistant to Mbol but was sensitive to Dpn 1 enzyme digestion, suggesting that this plasmid had retained its dam E. coli methylated sites and was therefore unable to undergo replication following transfection into homologous host cells. These results were discussed with relation to a previously described yeast cell cycle regulatory sequence which was functionally linked to an autonomous replicating sequence and was located near a yeast H2B gene.     

A positive regulatory sequence of the Saccharomyces cerevisiae ENO1 gene

ENO1-'lacZ fusions with various lengths of the ENO1 5'-flanking region were constructed on various types of yeast plasmid vectors. The fully expressed level of beta Gal directed by ENO1-'lacZ fusions differed depending on the type of vector, but on any type of vector, beta Gal activity was not greatly influenced by the carbon source in the medium. The 86-bp DNA region of ENO1 at position -487 to -402 upstream of the initiation codon, in which we had previously delimited the positive regulatory region of ENO1 (Uemura, H., Shiba, T., Paterson, M., Jigami, Y., & Tanaka, H. (1986) Gene 45, 67-75), exerted its function without requiring precise location with respect to the TATA box. The action of the positive regulatory region was not affected by its orientation. In addition, the substitution of the UASs of PHO5, encoding repressible acid phosphatase, with the regulatory region of ENO1 changed the expression of PHO5-'lacZ gene to constitutive, irrespective of the concentration of inorganic phosphate in the medium. Furthermore, the GCR1 gene cloned in a multicopy plasmid increased the expression of the ENO1-'lacZ fused genes.     

Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data

MOTIVATION: Biological processes in cells are properly performed by gene regulations, signal transductions and interactions between proteins. To understand such molecular networks, we propose a statistical method to estimate gene regulatory networks and protein-protein interaction networks simultaneously from DNA microarray data, protein-protein interaction data and other genome-wide data. RESULTS: We unify Bayesian networks and Markov networks for estimating gene regulatory networks and protein-protein interaction networks according to the reliability of each biological information source. Through the simultaneous construction of gene regulatory networks and protein-protein interaction networks of Saccharomyces cerevisiae cell cycle, we predict the role of several genes whose functions are currently unknown. By using our probabilistic model, we can detect false positives of high-throughput data, such as yeast two-hybrid data. In a genome-wide experiment, we find possible gene regulatory relationships and protein-protein interactions between large protein complexes that underlie complex regulatory mechanisms of biological processes.     

In vitro studies of the binding of the ARGR proteins to the ARG5,6 promoter.

ARGRI, ARGRII, and ARGRIII regulatory proteins control the expression of arginine anabolic and catabolic genes in Saccharomyces cerevisiae. We show here that they are also required in vitro to observe a protein-DNA complex with the promoter of the ARG5,6 gene. The specific binding of ARGR proteins in vitro is stimulated by arginine. Antibodies raised against a synthetic MCM1 polypeptide retard the migration of ARGR-DNA complex on gel mobility shift assays. This result suggests that MCM1 could be an additional regulatory element of arginine metabolism.     

Cloning and characterization of BCY1, a locus encoding a regulatory subunit of the cyclic AMP-dependent protein kinase in Saccharomyces cerevisiae.

We have cloned a gene (BCY1) from the yeast Saccharomyces cerevisiae that encodes a regulatory subunit of the cyclic AMP-dependent protein kinase. The encoded protein has a structural organization similar to that of the RI and RII regulatory subunits of the mammalian cyclic AMP-dependent protein kinase. Strains of S. cerevisiae with disrupted BCY1 genes do not display a cyclic AMP-dependent protein kinase in vitro, fail to grow on many carbon sources, and are exquisitely sensitive to heat shock and starvation.