Mechanism of DNA binding by the ADR1 zinc finger transcription factor as determined by SPR

Protein Engineering of Multi-Modular Transcription Factor Alcohol Dehydrogenase Repressor 1 (Adr1p), a Tool for Dissecting In Vitro Transcription Activation

Studying transcription machinery assembly in vitro is challenging because of long intrinsically disordered regions present within the multi-modular transcription factors. One example is alcohol dehydrogenase repressor 1 (Adr1p) from fermenting yeast, responsible for the metabolic switch from glucose to ethanol. The role of each individual transcription activation domain (TAD) has been previously studied, but their interplay and their roles in enhancing the stability of the protein is not known. In this work, we designed five unique miniAdr1 constructs containing either TADs I-II-III or TAD I and III, connected by linkers of different sizes and compositions. We demonstrated that miniAdr1-BL, containing only PAR-TAD I+III with a basic linker (BL), binds the cognate DNA sequence, located in the promoter of the ADH2 (alcohol dehydrogenase 2) gene, and is necessary to stabilize the heterologous expression. In fact, we found that the sequence of the linker between TAD I and III affected the solubility of free miniAdr1 proteins, as well as the stability of their complexes with DNA. miniAdr1-BL is the stable unit able to recognize ADH2 in vitro, and hence it is a promising tool for future studies on nucleosomal DNA binding and transcription machinery assembly in vitro.

Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding

A major challenge in obtaining a full molecular description of evolutionary adaptation is to characterize how transcription factor (TF) DNA-binding specificity can change. To identify mechanisms of TF diversification, we performed detailed comparisons of yeast C2H2 ZF proteins with identical canonical recognition residues that are expected to bind the same DNA sequences. Unexpectedly, we found that ZF proteins can adapt to recognize new binding sites in a modular fashion whereby binding to common core sites remains unaffected. We identified two distinct mechanisms, conserved across multiple Ascomycota species, by which this molecular adaptation occurred. Our results suggest a route for TF evolution that alleviates negative pleiotropic effects by modularly gaining new binding sites. These findings expand our current understanding of ZF DNA binding and provide evidence for paralogous ZFs utilizing alternate modes of DNA binding to recognize unique sets of noncanonical binding sites.

Analysis of DevR regulated genes in Mycobacterium tuberculosis

The DevRS two component system of Mycobacterium tuberculosis is responsible for its dormancy in host and becomes operative under hypoxic condition. It is experimentally known that phosphorylated DevR controls the expression of several downstream genes in a complex manner. In the present work we propose a theoretical model to show role of binding sites in DevR mediated gene expression. Individual and collective role of binding sites in regulating DevR mediated gene expression has been shown via modeling. Objective of the present work is twofold. First, to describe qualitatively the temporal dynamics of wild type genes and their known mutants. Based on these results we propose that DevR controlled gene expression follows a specific pattern which is efficient in describing other DevR mediated gene expression. Second, to analyze behavior of the system from information theoretical point of view. Using the tools of information theory we have calculated molecular efficiency of the system and have shown that it is close to the maximum limit of isothermal efficiency.

An investigation of the affinities, specificity and kinetics involved in the interaction between the Yin Yang 1 transcription factor and DNA

Human transcription factor Yin Yang 1 (YY1) is a four zinc-finger protein that regulates a large number of genes with various biological functions in processes such as development, carcinogenesis and B-cell maturation. The natural binding sites of YY1 are relatively unconserved and have a short core sequence (CCAT). We were interested in determining how YY1 recognizes its binding sites and achieves the necessary sequence selectivity in the cell. Using fluorescence anisotropy, we determined the equilibrium dissociation constants for selected naturally occurring YY1 binding sites that have various levels of similarity to the consensus sequence. We found that recombinant YY1 interacts with its specific binding sites with relatively low affinities from the high nanomolar to the low micromolar range. Using a fluorescence anisotropy competition assay, we determined the affinity of YY1 for non-specific DNA to be between 30 and 40 μm, which results in low specificity ratios of between 3 and 220. Additionally, surface plasmon resonance measurements showed rapid association and dissociation rates, suggesting that the binding strength is regulated through changes in both k(a) and k(d). In conclusion, we propose that, in the cell, YY1 may achieve higher specificity by associating with co-regulators or as a part of multi-subunit complexes.

14-3-3 (Bmh) proteins inhibit transcription activation by Adr1 through direct binding to its regulatory domain

14-3-3 proteins, known as Bmh in yeast, are ubiquitous, highly conserved proteins that function as adaptors in signal transduction pathways by binding to phosphorylated proteins to activate, inactivate, or sequester their substrates. Bmh proteins have an important role in glucose repression by binding to Reg1, the regulatory subunit of Glc7, a protein phosphatase that inactivates the AMP-activated protein kinase Snf1. We describe here another role for Bmh in glucose repression. We show that Bmh binds to the Snf1-dependent transcription factor Adr1 and inhibits its transcriptional activity. Bmh binds within the regulatory domain of Adr1 between amino acids 215 and 260, the location of mutant ADR1(c) alleles that deregulate Adr1 activity. This provides the first explanation for the phenotype resulting from these mutations. Bmh inhibits Gal4-Adr1 fusion protein activity by binding to the Ser230 region and blocking the function of a nearby cryptic activating region. ADR1(c) alleles, or the inactivation of Bmh, relieve the inhibition and Snf1 dependence of this activating region, indicating that the phosphorylation of Ser230 and Bmh are important for the inactivation of Gal4-Adr1. The Bmh binding domain is conserved in orthologs of Adr1, suggesting that it acquired an important biological function before the whole-genome duplication of the ancestor of S. cerevisiae.

New insights into DNA-binding behavior of Wilms tumor protein (WT1)--a dual study

Wilms Tumor suppressor protein (WT1) is a transcription factor that is involved in a variety of developmental functions during organ development. It is also implicated in the pathology of several different cancer forms. The protein contains four C(2)H(2)-type zinc fingers and it specifically binds GC-rich sequences in the promoter regions of its target genes, which are either up or down regulated. Two properties make WT1 a more unusual transcription factor - an unconventional amino acid composition for zinc finger 1, and the insertion of a tri-peptide KTS in some of the splice isoforms of WT1. Using six WT1 constructs in which zinc fingers are systematically deleted, a dual study based on a bacterial 1-hybrid system and surface plasmon resonance measurements is performed. The experiments show that the effect of zinc finger 1 is not significant in terms of overall DNA-binding kinetics, however it influences both the specificity of target recognition and stability of interaction in presence of KTS. The KTS insertion, however, only mildly retards binding affinity, mainly by affecting the on-rate. We suggest that the insertion disturbs zinc finger 4 from its binding frame, thus weakening the rate of target recognition. Finally, for the construct in which both zinc fingers 1 and 4 were deleted, the two middle fingers 2-3 still could function as a 'minimal DNA-recognition domain' for WT1, however the formation of a stable protein-DNA complex is impaired since the overall affinity was dramatically reduced mainly since the off-rate was severely affected.

Promoter binding by the Adr1 transcriptional activator may be regulated by phosphorylation in the DNA-binding region

BACKGROUND

Post-translational modification regulates promoter-binding by Adr1, a Zn-finger transcriptional activator of glucose-regulated genes. Support for this model includes the activation of an Adr1-dependent gene in the absence of Adr1 protein synthesis, and a requirement for the kinase Snf1 for Adr1 DNA-binding. A fusion protein with the Adr1 DNA-binding domain and a heterologous activation domain is glucose-regulated, suggesting that the DNA binding region is the target of regulation.

METHODOLOGY/PRINCIPAL FINDINGS

Peptide mapping identified serine 98 adjacent to the Zn-fingers as a phosphorylation site. An antibody specific for phosphorylated serine 98 on Adr1 showed that the level of phosphorylated Adr1 relative to the level of total Adr1 decreased with glucose derepression, in a Snf1-dependent manner. Relative phosphorylation decreased in a PHO85 mutant, and this mutant constitutively expressed an Adr1-dependent reporter. Pho85 did not phosphorylate Adr1 in vitro, suggesting that it affects Adr1 indirectly. Mutation of serine 98 to the phosphomimetic amino acid aspartate reduced in vitro DNA-binding of the recombinant Adr1 DNA-binding domain. Mutation to aspartate or alanine affected activation of a reporter by full-length Adr1, and in vivo promoter binding.

CONCLUSIONS/SIGNIFICANCE

Mutation of Adr1 serine 98 affects in vitro and in vivo DNA binding, and phosphorylation of serine 98 in vivo correlates with glucose availability, suggesting that Adr1 promoter-binding is regulated in part by serine 98 phosphorylation.

Transition state for protein-DNA recognition

We describe the formation of protein-DNA contacts in the two-state route for DNA sequence recognition by a transcriptional regulator. Surprisingly, direct sequence readout establishes in the transition state and constitutes the bottleneck of complex formation. Although a few nonspecific ionic interactions are formed at this early stage, they mainly play a stabilizing role in the final consolidated complex. The interface is fairly plastic in the transition state, likely because of a high level of hydration. The overall picture of this two-state route largely agrees with a smooth energy landscape for binding that speeds up DNA recognition. This "direct" two-state route differs from the parallel multistep pathway described for this system, which involves nonspecific contacts and at least two intermediate species that must involve substantial conformational rearrangement in either or both macromolecules.

Identification of a minimal cre1 promoter sequence promoting glucose-dependent gene expression in the beta-lactam producer Acremonium chrysogenum

The promoter of the cre1 gene, encoding the glucose-dependent regulator CRE1 from the beta-lactam producer Acremonium chrysogenum, carries 15 putative CRE1 binding sites (BS1 to BS15). For a detailed analysis, we fused cre1 promoter deletion derivatives with the DsRed reporter gene to perform a comparative gene expression analysis. Plate assays, Northern hybridizations, and spectrofluorometric measurements of DsRed identified the minimal D4 promoter sequence that promoted glucose-dependent expression. Truncated recombinant CRE1 interacted with D4 in electromobility shift analysis and these binding studies were further extended with two oligonucleotides, carrying putative CRE1 binding sites BS14 and BS15. Surface plasmon resonance analysis was performed using BS14 and BS15, along with four derivatives containing 2 or 4 bp substitutions within BS14 and BS15, respectively. Substitutions within BS14 abolished the high affinity interaction with CRE1, while mutations in BS15 only marginally diminished the affinity with CRE1. In vivo analysis of a modified D4 sequence with substitutions in the two binding sites confirmed the in vitro binding results and still promoted glucose-dependent gene expression. Our results will contribute to the construction of versatile expression vectors carrying a minimal cre1 promoter sequence that still confers glucose-dependent induction of gene expression.

Correlation between binding rate constants and individual information of E. coli Fis binding sites

Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics appear to be inaccessible from sequence information since the relative contributions of the on- and off-rates to the binding constant, and hence the free energy, are unknown. However, the on-rate could be independent of the sequence since a protein is likely to bind once it is near a site. To test this, we used surface plasmon resonance and electromobility shift assays to determine the kinetics for binding of the Fis protein to a range of naturally occurring binding sites. We observed that the logarithm of the off-rate is indeed proportional to the individual information of the binding sites, as predicted. However, the on-rate is also related to the information, but to a lesser degree. We suggest that the on-rate is mostly determined by DNA bending, which in turn is determined by the sequence information. Finally, we observed a break in the binding curve around zero bits of information. The break is expected from information theory because it represents the coding demarcation between specific and nonspecific binding.

Engineering Zinc Finger Protein Transcription Factors: The Therapeutic Relevance of Switching Endogenous Gene Expression On or Off at Command

Modulating gene expression directly at the DNA level represents a novel approach to control cellular processes. In this respect, zinc finger protein DNA-binding domains can be engineered to target virtually any gene. Coupling of a transcription activation or repression domain to these zinc fingers permits regulating gene expression at will, providing a platform of unlimited therapeutic applications. In this review, steps involved in the engineering of zinc finger protein transcription factors are described. In addition, an overview of endogenous genes successfully targeted for modulating expression by engineered zinc finger protein transcription factors is given. So far, research has mainly focused on targeting genes involved in cancer and angiogenesis, with encouraging evaluation in vivo and progression into a clinical trial. Altogether, engineered zinc finger proteins offer a new and exciting direction in the field of medical research with promising prospects.

Genome-wide transcription profiling of the early phase of biofilm formation by Candida albicans

The ability to adhere to surfaces and develop as a multicellular community is an adaptation used by most microorganisms to survive in changing environments. Biofilm formation proceeds through distinct developmental phases and impacts not only medicine but also industry and evolution. In organisms such as the opportunistic pathogen Candida albicans, the ability to grow as biofilms is also an important mechanism for persistence, facilitating its growth on different tissues and a broad range of abiotic surfaces used in medical devices. The early stage of C. albicans biofilm is characterized by the adhesion of single cells to the substratum, followed by the formation of an intricate network of hyphae and the beginning of a dense structure. Changes in the transcriptome begin within 30 min of contact with the substrate and include expression of genes related to sulfur metabolism, in particular MET3, and the equivalent gene homologues of the Ribi regulon in Saccharomyces cerevisiae. Some of these changes are initiated early and maintained throughout the process; others are restricted to the earliest stages of biofilm formation. We identify here a potential alternative pathway for cysteine metabolism and the biofilm-associated expression of genes involved in glutathione production in C. albicans.

Survey of the year 2003 commercial optical biosensor literature

In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.

Effects of length and position of an extended linker on sequence-selective DNA recognition of zinc finger peptides

Engineered zinc finger proteins revealed that a linker sequence connecting zinc finger units has a significant effect on the DNA binding property of the protein. The recognition for a noncontiguous DNA target beyond the current recognition code of zinc finger proteins has never been determined because of the limitation of a zinc finger framework. DNA recognition of zinc finger proteins is limited only to a contiguous subset of three base pairs. We propose the recognition for a noncontiguous DNA target by inserting amino acids into the canonical linker between zinc finger units. The sequence selectivity of the new zinc finger peptides was evaluated by gel mobility shift assays. DNase I footprinting analyses clearly showed different DNA binding of various linker-extended zinc finger peptides. The application of a SPR measurement also revealed a DNA sequence selectivity of peptides. Insertion of three amino acids is enough for recognition of a noncontiguous DNA target with sequence selectivity. An extended linker will be useful for expansion of the recognition code of zinc finger proteins and for development of a new role for linker sequences in DNA binding of zinc finger proteins.