Molecular architecture of a Leu3p-DNA complex in solution: a biochemical approach

Leucine biosynthesis in fungi: entering metabolism through the back door

After exploring evolutionary aspects of branched-chain amino acid biosynthesis, the review focuses on the extended leucine biosynthetic pathway as it operates in Saccharomyces cerevisiae. First, the genes and enzymes specific for the leucine pathway are considered: LEU4 and LEU9 (encoding the alpha-isopropylmalate synthase isoenzymes), LEU1 (isopropylmalate isomerase), and LEU2 (beta-isopropylmalate dehydrogenase). Emphasis is given to the unusual distribution of the branched-chain amino acid pathway enzymes between mitochondrial matrix and cytosol, on the newly defined role of Leu5p, and on regulatory mechanisms governing gene expression and enzyme activity, including new evidence for the metabolic importance of the regulation of alpha-isopropylmalate synthase by coenzyme A. Next, structure-function relationships of the transcriptional regulator Leu3p are addressed, defining its dual role as activator and repressor and discussing evidence in support of the self-masking model. Recent data pointing at a more extended Leu3p regulon are discussed. An overview of the layered controls of the extended leucine pathway is provided that includes a description of the newly recognized roles of Ilv5p and Bat1p in maintaining mitochondrial integrity. Finally, branched-chain amino acid biosynthesis and its regulation in other fungi are summarized, the question of leucine as metabolic signal is addressed, and possible directions of future research in this area are outlined.

FacB, the Aspergillus nidulans activator of acetate utilization genes, binds dissimilar DNA sequences

The facB gene is required for acetate induction of acetamidase (amdS) and the acetate utilization enzymes acetyl-CoA synthase (facA), isocitrate lyase (acuD) and malate synthase (acuE) in Aspergillus nidulans. The facB gene encodes a transcriptional activator with a GAL4-type Zn(II)2Cys6 zinc binuclear cluster DNA-binding domain which is shown to be required for DNA binding. In vitro DNA-binding sites for FacB in the 5' regions of the amdS, facA, acuD and acuE genes have been identified. Mutations in amdS FacB DNA-binding sites affected expression of an amdS-lacZ reporter in vivo and altered the affinity of in vitro DNA binding. This study shows that the FacB Zn(II)2Cys6 cluster binds to dissimilar sites which show similarity in form but not sequence with DNA-binding sites of other Zn(II)2Cys6 proteins. Sequences with homology to FacB sites are found in the 5' regions of genes regulated by the closely related yeast Zn(II)2Cys6 protein CAT8.

Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators

The C6 zinc cluster family of fungal regulatory proteins shares as DNA-binding motif the C6 zinc cluster, also known as the Zn(II)2Cys6 binuclear cluster. This family includes transcriptional activators like Gal4p, Leu3p, Hap1p, Put3p and Cha4p from Saccharomyces cerevisiae, qutA and amdR from Aspergillus, nit4 from Neurospora and Ntf1 from Schizosaccharomyces pombe. Seventy-nine proteins were retrieved from databases by homology to the C6 zinc cluster. All were fungal and 56 were found in the entire genome sequence of S.cerevisiae. Sequence analysis suggests that 60 of the 79 proteins possess one or more coiled-coil dimerization regions succeeding the C6 zinc cluster. Previous comparisons of Gal4p and seven other C6 zinc cluster proteins identified an additional region with weak homology. This region, designated the middle homology region (MHR), was shown to be present in 50 of the 79 proteins. Although reported mutation and deletion analyses suggest a role of MHR in regulation of protein activity, no function has yet been assigned specifically to this region. We find that the family of MHR sequences is confined to C6 zinc cluster proteins and hypothesize that one MHR function is to assist the C6 zinc cluster in DNA target discrimination.

A novel DNA binding motif for yeast zinc cluster proteins: the Leu3p and Pdr3p transcriptional activators recognize everted repeats

The Gal4, Put3, and Ppr1 yeast zinc cluster proteins bind as homodimers to DNA sequences composed of palindromic CGG triplets. Spacing between the triplets specifies the target site for a given zinc cluster protein. In addition, Hap1p, another zinc cluster protein, also recognizes CGG triplets but only when oriented as a direct repeat. Unexpectedly, our results show that Leu3p, another member of this family, also recognizes CGG triplets but oriented in opposite directions and spaced by 4 nucleotides (an everted repeat or inverted palindrome: CCG-N4-CGG). This constitutes a novel DNA motif for zinc cluster proteins. Moreover, the presence of this motif was shown to be essential for in vivo activation by Leu3p of a minimal reporter containing one copy of a target site for this activator. We also provide evidence that another member of this family, Pdr3p, binds to an everted repeat spaced by 0 nucleotides (CCGCGG). Thus, our results show that three CGG motifs are used by members of the zinc cluster family: palindromes, direct repeats, and everted repeats.

Transcriptional corepression in vitro: a Mot1p-associated form of TATA-binding protein is required for repression by Leu3p

Signals from transcriptional activators to the general mRNA transcription apparatus are communicated by factors associated with RNA polymerase II or the TATA-binding protein (TBP). Currently, little is known about how gene-specific transcription repressors communicate with RNA polymerase II. We have analyzed the requirements for repression by the saccharomyces cerevisiae Leu3 protein (Leu3p) in a reconstituted transcription system. We have identified a complex form of TBP which is required for communication of the repressing signal. This TFIID-like complex contains a known TBP-associated protein, Mot1p, which has been implicated in the repression of a subset of yeast genes by genetic analysis. Leu3p-dependent repression can be reconstituted with purified Mot1p and recombinant TBP. In addition, a mutation in the Mot1 gene leads to partial derepression of the Leu3p-dependent LEU2 promoter. These in vivo and in vitro observations define a role for Mot1p as a transcriptional corepressor.

Detection of leucine-independent DNA site occupancy of the yeast Leu3p transcriptional activator in vivo

The product of the Saccharomyces cerevisiae LEU3 gene, Leu3p, is a transcriptional activator which regulates leucine biosynthesis in response to intracellular levels of leucine through the biosynthetic intermediate alpha-isopropylmalate. We devised a novel assay to examine the DNA site occupancy of Leu3p under different growth conditions, using a reporter gene with internal Leu3p-binding sites. Expression of the reporter is inhibited by binding of nuclear Leu3p to these sites; inhibition is dependent on the presence of the sites in the reporter, on the integrity of the Leu3p DNA-binding domain, and, surprisingly, on the presence of a transcriptional activation domain in the inhibiting protein. By this assay, Leu3p was found to occupy its binding site under all conditions tested, including high and low levels of leucine and in the presence and absence of alpha-isopropylmalate. The localization of Leu3p to the nucleus was confirmed by immunofluorescence staining of cells expressing epitope-tagged Leu3p derivatives. We conclude that Leu3p regulates transcription in vivo without changing its intracellular localization and DNA site occupancy.