Purification and structural characterization of transcriptional regulator Leu3 of yeast

A "Hit and Run" Approach to Inducible Direct Reprogramming of Astrocytes to Neural Stem Cells

Temporal and spatial control of gene expression can be achieved using an inducible system as a fundamental tool for regulated transcription in basic, applied and eventually in clinical research. We describe a novel “hit and run” inducible direct reprogramming approach. In a single step, 2 days post-transfection, transiently transfected Sox2^FLAG under the Leu3p-αIPM inducible control (iSox2) triggers the activation of endogenous Sox2, redirecting primary astrocytes into abundant distinct nestin-positive radial glia cells. This technique introduces a unique novel tool for safe, rapid and efficient reprogramming amendable to regenerative medicine.

A novel protein that binds to dnrN-dnrO intergenic region of Streptomyces peucetius purified by DNA affinity capture has dihydrolipoamide dehydrogenase activity

An antitumour chemotherapeutic, daunorubicin (DNR), produced by Streptomyces peucetius exhibits cytotoxic activity through topoisomerase-mediated interaction with DNA, thereby inhibiting DNA replication and repair and RNA and protein synthesis. It is synthesized by the type II polyketide pathway. Understanding molecular mechanisms that drive expression of antibiotic biosynthetic genes in response to diverse signals and chemical inducers is of considerable interest. Intergenic DNA between regulatory genes dnrN and dnrO of DNR biosynthesis pathway in S. peucetius has a promoter for transcription of dnrN in one strand and three promoters in the opposite strand for dnrO. Studies have shown that DnrO binds to a specific sequence in this region to activate transcription of dnrN. In the present study, using biotinylated intergenic DNA in combination with streptavidin magnetic beads, we have purified a protein that binds to this target sequence. The protein has been characterized by nano LC ESI MS/MS mass spectrometry. Sequence similarity searches for effective identification of protein by genome databases comparisons led to identification of a sequence-specific DNA binding protein that exhibits dihydrolipoamide dehydrogenase (DLDH) activity suggesting that this protein may be involved in regulation of DNR biosynthesis.

Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions

Modern computational methods are revealing putative transcription-factor (TF) binding sites at an extraordinary rate. However, the major challenge in studying transcriptional networks is to map these regulatory element predictions to the protein transcription factors that bind them. We have developed a microarray-based profiling of phage-display selection (MaPS) strategy that allows rapid and global survey of an organism's proteome for sequence-specific interactions with such putative DNA regulatory elements. Application to a variety of known yeast TF binding sites successfully identified the cognate TF from the background of a complex whole-proteome library. These factors contain DNA-binding domains from diverse families, including Myb, TEA, MADS box, and C2H2 zinc-finger. Using MaPS, we identified Dot6 as a trans-active partner of the long-predicted orphan yeast element Polymerase A & C (PAC). MaPS technology should enable rapid and proteome-scale study of bi-molecular interactions within transcriptional networks.

Specific interactions between protein transcription factors (TFs) and their DNA recognition sites are central to the regulation of gene expression. Inter-species conservation of these TF binding sites (TFBS), and their statistical enrichment in sets of co-expressed genes, facilitates their large-scale prediction through computational sequence analysis. A major challenge in characterizing these putative TFBS is the identification of the proteins that bind them. We have developed a new approach to this problem by expressing random genomically encoded protein fragments as fusions to the capsid of bacteriophage T7. We select this diverse phage-display “library” for binding surface-immobilized instances of the TFBS in the form of short double-stranded DNA. This in vitro selection strategy leads to the enrichment of phage whose capsid-fusion peptides interact with the specific DNA sequence. Because each phage carries the DNA encoding the peptide fusion, the identity of the enriched phage can be determined through population-level PCR amplification of DNA inserts and their hybridization to DNA microarrays. Here, we show that this technology efficiently reveals the identity of proteins that bind known and novel predicted regulatory elements. Its application to a predicted yeast element (PAC) reveals Dot6 as one of its interaction partners, both in vitro and within the yeast nucleus.

Methods for transcription factor separation

Recent advances in the separation of transcription factors (TFs) are reviewed in this article. An overview of the transcription factor families and their structure is discussed and a computer analysis of their sequences reveals that while they do not differ from other proteins in molecular mass or isoelectric pH, they do differ from other proteins in the abundance of certain amino acids. The chromatographic and electrophoretic methods which have been successfully used for purification and analysis are discussed and recent advances in stationary and mobile phase composition is discussed.

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.

Binding and activation by the zinc cluster transcription factors of Saccharomyces cerevisiae. Redefining the UASGABA and its interaction with Uga3p

Uga3p, a member of zinc binuclear cluster transcription factor family, is required for gamma-aminobutyric acid-dependent transcription of the UGA genes in Saccharomyces cerevisiae. Members of this family bind to CGG triplets with the spacer region between the triplets being an important specificity determinant. A conserved 19-nucleotide activation element in certain UGA gene promoter regions contains a CCGN(4)CGG-everted repeat proposed to be the binding site of Uga3p, UAS(GABA). The function of conserved nucleotides flanking the everted repeat has not been rigorously investigated. The interaction of Uga3p with UAS(GABA) was characterized in terms of binding in vitro and transcriptional activation of lacZ reporter genes in vivo. Electromobility shift assays using mutant UAS(GABA) sequences and heterologously produced full-length Uga3p demonstrated that UAS(GABA) consists of two independent Uga3p binding sites. Simultaneous occupation of both Uga3p binding sites of UAS(GABA) with high affinity is essential for GABA-dependent transcriptional activation in vivo. We present evidence that the two Uga3p molecules bound to UAS(GABA) probably interact with each other and show that Uga3p((1-124)), previously used for binding studies, is not functionally equivalent to the full-length protein with respect to binding in vitro. We propose that the Uga3p binding site is an asymmetric site of 5'-SGCGGNWTTT-3' (S = G or C, W = A, or T and n = no nucleotide or G). However, UAS(GABA), is a palindrome containing two asymmetric Uga3p binding sites.

Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities

DNA-binding proteins regulate gene expression by binding preferentially to a set of related sequences. In order to quantify the correlation between gene regulation and the presence of sequence motifs, the affinity of a transcription factor for each variant of the binding site must be known or predicted. In addition, the contribution of multiple binding sites to the regulation of a single gene must be modeled. To predict the affinity of the yeast Leu3 transcription factor for genomic-binding sites, we measured the in vitro equilibrium dissociation constants of 43 binding-site variants and established that the free energy of binding can be approximated as a sum of free energy contributions from each base-pair. This allows the prediction of an equilibrium dissociation constant for all potential binding sites in the genome and, therefore, their fractional occupancy at some assumed concentration of free Leu3. From the occupancy of individual sites, the probability that at least one site is occupied within a defined segment upstream of a gene was calculated for all genes in yeast. We find that this probability is substantially better correlated with regulation by Leu3 than is the number of binding sites. This is true whether the number of binding sites is based on a consensus site definition of the binding site or by enumeration of all variants that have a predicted K(d) value below some threshold. The occupancy calculation was best able to rationalize the Leu3-regulated gene set over a Leu3 concentration range that spans the K(d) values for the best sites.

Conformational changes play a role in regulating the activity of the proline utilization pathway-specific regulator in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the ability to use proline as a nitrogen source requires the Put3p transcriptional regulator, which turns on the expression of the proline utilization genes, PUT1 and PUT2, in the presence of the inducer proline and in the absence of preferred nitrogen sources. Changes in target gene expression occur through an alteration in activity of the DNA-bound Put3p, a member of the Zn(II)2Cys6 binuclear cluster family of proteins. Here, we report that the 'on' conformation can be mimicked in the absence of proline by the insertion of an epitope tag in several different places in the protein, as well as by specific amino acid changes that suppress a put3 mutation leading to non-inducibility of the pathway. In addition, the presence of proline causes a conformational change in the Put3 protein detected by increased sensitivity to thrombin or V8 protease. These findings suggest that Put3p shifts from an inactive to an activate state via conformational changes.

Yeast transcriptional regulator Leu3p. Self-masking, specificity of masking, and evidence for regulation by the intracellular level of Leu3p

Recent work suggests that the masking of the activation domain (AD) of yeast transactivator Leu3p, observed in the absence of the metabolic signal alpha-isopropylmalate, is an intramolecular event. Much of the evidence came from the construction and analysis of a mutant form of Leu3p (Leu3-dd) whose AD is permanently masked (Wang, D., Hu, Y., Zheng, F., Zhou, K., and Kohlhaw, G. B. (1997) J. Biol. Chem. 272, 19383-19392). In a modified two-hybrid experiment, the ADs of both wild type Leu3p and Leu3-dd were shown to interact with the remainder of the Leu3 protein, in an alpha-isopropylmalate-dependent manner. The finding that masking and unmasking proceed apparently normally when full-length Leu3p is expressed in mammalian cells is also consistent with the notion of intramolecular masking. Here we report on the identification of nine missense mutations (all of them suppressors of the Leu3-dd phenotype) that cause permanent unmasking of Leu3p. The nine mutations map to three short segments located within a 140-residue-long region of the C-terminal part of the middle region of Leu3p. These segments may be part of a spatial trap for the AD. We also performed "domain swaps" between Leu3p and Cha4p, a serine/threonine-responsive activator that, like Leu3p, belongs to the family of Zn(II)2Cys6 proteins. We show that AD masking and response to the appropriate metabolic signal only occur when a given AD remains attached to its own middle region; middle region swapping results in constitutively active proteins. Finally, we show that the extent to which Leu3p regulates reporter gene expression depends on the intracellular concentration of Leu3p. The possible physiological significance of this observation is discussed in light of the known regulation of Leu3p by Gcn4p.

Regulation of expression of the amino acid transporter gene BAP3 in Saccharomyces cerevisiae

The BAP3 gene of Saccharomyces cerevisiae encodes a protein with a high similarity to the BAP2 gene product, a high-affinity permease for branched-chain amino acids. In this paper, we show that, like BAP2, the expression of the BAP3 gene in S. cerevisiae is induced by the addition of branched-chain amino acids to the medium. Unexpectedly, most other naturally occurring L-amino acids found in proteins (with the exception of proline, lysine, arginine and histidine) have the same effect on the expression of BAP3. The induction of BAP3 expression appears to be dependent on Stp1p, a nuclear protein, previously shown to be involved in pre-tRNA maturation and also required for the expression of BAP2, as induction is no longer observed in an stp1 - mutant. The transcriptional regulator Leu3p is not involved in the induction of BAP3 expression, but may act as a repressor of BAP3 expression in the absence of leucine, as can be inferred from a transcriptional analysis in a Deltaleu3 mutant. By extensive deletion analysis of the BAP3 promoter fused to a GUS reporter, as well as by fusions of different parts of the BAP3 promoter to a LacZ reporter, we have found that a portion of the BAP3 promoter from - 418 to - 392 relative to the ATG start codon is both necessary and sufficient for the Stp1p-dependent induction of BAP3 expression by (most) amino acids. We have therefore named this sequence UASaa (amino acid-dependent upstream activator sequence). Neither Stp1p nor Leu3p appear to bind to the UASaa, at least in vitro, as judged from gel retardation assays. Sequences similar to the UASaa can be found in the promoters of BAP2, PTR2 and TAT1; genes that, like BAP3, encode permeases inducible by amino acids, suggesting that amino acid induction of all these genes is exerted via a common mechanism.

Evidence that intramolecular interactions are involved in masking the activation domain of transcriptional activator Leu3p

The Leu3 protein of Saccharomyces cerevisiae regulates the expression of genes involved in branched chain amino acid biosynthesis and in ammonia assimilation. It is modulated by alpha-isopropylmalate, an intermediate in leucine biosynthesis. In the presence of alpha-isopropylmalate, Leu3p is a transcriptional activator. In the absence of the signal molecule, the activation domain is masked, and Leu3p acts as a repressor. The recent discovery that Leu3p retains its regulatory properties when expressed in mammalian cells (Guo, H., and Kohlhaw, G. B. (1996) FEBS Lett. 390, 191-195) suggests that masking and unmasking of the activation domain occur without the participation of auxiliary proteins. Here we present experimental support for this notion and address the mechanism of masking. We show that modulation of Leu3p is exceedingly sensitive to mutations in the activation domain. An activation domain double mutant (D872N/D874N; designated Leu3-dd) was constructed that has the characteristics of a permanently masked activator. Using separately expressed segments containing either the DNA binding domain-middle region or the activation domain of wild type Leu3p (or Leu3-dd) in a modified yeast two-hybrid system, we provide direct evidence for alpha-isopropylmalate-dependent interaction between these segments. Finally, we use the phenotype of Leu3-dd-containing cells (slow growth in the absence of added leucine) to select for suppressor mutations that map to the middle region of Leu3-dd. The properties of nine such suppressors further support the idea that masking is an intramolecular process and suggest a means for mapping the surface involved in masking.

Regulation of transcription in mammalian cells by yeast Leu3p and externally supplied inducer

The Leu3 protein of yeast is a dual-function regulator, stimulating transcription when the inducer alpha-isopropylmalate (alpha-IPM) is present and suppressing transcription when the inducer is absent. Here we show that Leu3p retains both its positive and negative regulatory properties when expressed in mammalian cells or when added to a mammalian nuclear extract. Alpha-IPM stimulates reporter gene expression 15-20-fold, both in vivo and in vitro. The concentration of alpha-IPM required for half-maximal stimulation in vitro is 2.5 x 10(-4) M. No yeast-specific factors other than Leu3p itself are required for up- or down-regulation. Since alpha-IPM is not metabolized in mammalian cells, the Leu3p-alpha-IPM system might be useful in gene therapy and other studies as a highly specific, externally controlled on/off switch of gene expression.