In Vitro selection of DNA binding sites for transcription factor, PhaR, from Paracoccus denitrificans using genetic library on microbeads and flow cytometry

Ultra-high-throughput analysis of functional biomolecules using in vitro selection and bioinformatics

Functional analysis of biomolecules, including nucleic acids and proteins, is important for understanding biological mechanisms in living cells such as gene expression and metabolism. To analyze diverse biomolecular functions, large-scale screening systems for biomolecules have been developed for various applications such as to improve enzyme activity and identify target binding molecules. One of these systems, the Bead Display system, utilizes emulsion technology and is a powerful tool for rapidly screening functional nucleic acids or proteins in vitro. Furthermore, an analytical pipeline that consists of genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq, gene expression analysis, and bioinformatics was shown to be a robust platform for comprehensively identifying genes regulated by a transcription factor. This review provides an overview of the biomolecular screening methods developed to date.

Monitoring and kinetic analysis of the molecular interactions by which a repressor protein, PhaR, binds to target DNAs and poly[(R)-3-hydroxybutyrate]

The repressor protein PhaR, which is a component of poly[(R)-3-hydroxybutyrate] granules, functions as a repressor of the gene expression of the phasin PhaP and of PhaR itself. We used a quartz crystal microbalance to investigate the binding behavior by which PhaR in Ralstonia eutropha H16 targets DNAs and amorphous poly[(R)-3-hydroxybutyrate] thin films. Binding rate constants, dissociation rate constants, and dissociation constants of the binding of PhaR to DNA and to amorphous poly[(R)-3-hydroxybutyrate] suggested that PhaR bind to both in a similar manner. On the basis of the binding rate constant values, we proposed that the phaP gene would be derepressed in harmony with the ratio of the concentration of the target DNA to the concentration of amorphous poly[(R)-3-hydroxybutyrate] at the start of poly[(R)-3-hydroxybutyrate] synthesis in R. eutropha H16.

High-throughput screening method for promoter activity using bead display and a ligase ribozyme

In this report, we describe the development of a novel in vitro high-throughput system for detecting and screening promoter activity; the method employs emulsified reactions and a ligase ribozyme. In our study, a promoter DNA fragment containing the ribozyme gene was immobilized on a bead by using emulsion PCR, followed by in vitro transcription of the immobilized DNA in water-in-oil emulsions. Owing to the self-ligation activity of the ribozyme, it was co-transcriptionally linked to the active promoter immobilized on the beads. The bead complex containing the active promoter sequence was then labeled by reverse transcription with a fluorescently labeled primer. Employing flow cytometry, the fluorescence intensity corresponding to the strength of each promoter was observed, indicating the applicability of the system for promoter evaluation. Moreover, two rounds of screening with T7 RNA polymerase using a cell sorter enriched the T7 promoter fragment by 70 folds from a 1:100 mixture of T7 promoter and SP6 promoter fragments, suggesting that this system can be used to screen promoters.

Comprehensive analysis of the DNA-binding specificity of an Aspergillus nidulans transcription factor, AmyR, using a bead display system

The in vitro DNA binding profile of Aspergillus nidulans transcription factor AmyR was analyzed by a novel approach employing a genetic library of beads and flow cytometry analysis. An artificial library with 22 randomized nucleotides was constructed and subjected to a protein-DNA binding reaction with MalE-tagged AmyR. DNA fragments with potential AmyR-binding sites were labeled with fluorescence-conjugated antibody to be enriched by flow cytometry through 5 rounds of successive selection. Finally, a binding motif with a single CGG triplet was obtained from DNA fragments showing weak AmyR binding, while another motif with dual CGG triplets was discovered with stronger binding fragments. An informative motif, CGGNNNTTTNTCGG, was found to exist only in the promoter region of highly AmyR-dependent genes. These results suggest that this system is a powerful tool for the rapid and comprehensive analysis of the binding preferences of transcription factors.

GLOBE: Analysis of DNA-protein interaction analysis

Emulsion PCR, a hyper, multi, parallel PCR in water-phase droplets in water-in-oil (w/o) emulsion, can be used to make a genetic l ibrary on beads (GLOBE). In GLOBE, we have developed a novel high-throughput screening system for the analysis of the recognition sequences of DNA-binding proteins, which can be prepared by using either an in vivo or an in vitro protein synthesis system. The system can contribute to the low-cost comprehensive analysis of transcription factor-binding regions.

Identification of hookworm DAF-16/FOXO response elements and direct gene targets

BACKGROUND

The infective stage of the parasitic nematode hookworm is developmentally arrested in the environment and needs to infect a specific host to complete its life cycle. The canine hookworm (Ancylostoma caninum) is an excellent model for investigating human hookworm infections. The transcription factor of A. caninum, Ac-DAF-16, which has a characteristic fork head or "winged helix" DNA binding domain (DBD), has been implicated in the resumption of hookworm development in the host. However, the precise roles of Ac-DAF-16 in hookworm parasitism and its downstream targets are unknown. In the present study, we combined molecular techniques and bioinformatics to identify a group of Ac-DAF-16 binding sites and target genes.

METHODOLOGY/PRINCIPAL FINDINGS

The DNA binding domain of Ac-DAF-16 was used to select genomic fragments by in vitro genomic selection. Twenty four bound genomic fragments were analyzed for the presence of the DAF-16 family binding element (DBE) and possible alternative Ac-DAF-16 bind motifs. The 22 genes linked to these genomic fragments were identified using bioinformatics tools and defined as candidate direct gene targets of Ac-DAF-16. Their developmental stage-specific expression patterns were examined. Also, a new putative DAF-16 binding element was identified.

CONCLUSIONS/SIGNIFICANCE

Our results show that Ac-DAF-16 is involved in diverse biological processes throughout hookworm development. Further investigation of these target genes will provide insights into the molecular basis by which Ac-DAF-16 regulates its downstream gene network in hookworm infection.

High-throughput screening of DNA binding sites for transcription factor AmyR from Aspergillus nidulans using DNA beads display system

We established a high-throughput screening method for the DNA binding sequence of a eukaryotic transcription factor by using the bead display system with emulsion PCR and flow cytometry and applied it for identifying a eukaryotic transcriptional activator AmyR, which is known to regulate amylolytic gene expression in Aspergillus species. Segmented parts of the binding site of AmyR were randomized to make a DNA library on beads, onto which MalE-tagged AmyR protein and fluorescent anti-MalE tag antibody were bound, followed by selection with a flow cytometer. From a library replacing well-conserved six nucleotides (CGG-CGG) to random ones, the consensus sequence was recovered at a high frequency, demonstrating the reliability of the screening system. Interestingly, similar analysis for another library having randomized intermediate eight nucleotides between the conserved triplets revealed that the selected intermediate sequence had a strong preference for the T nucleotide. Moreover, exactly the same sequence with the upstream region of amyB, a typical AmyR-regulated gene, was found in the selection. These results suggest that this screening system will be a powerful tool for high-throughput analysis of the eukaryotic transcriptome.

Directed evolution of angiotensin II-inhibiting peptides using a microbead display

Angiotensin II (ang II), an octapeptide (DRVYVHPF), can regulate blood pressure by binding specifically to its receptor, AT1. A peptide (VVIVIY) in the first transmembrane of AT1 has been found, via peptide array technology, to have an affinity for ang II. In this study, the peptide P2, which contained the VVIVIY sequence, was mutated and screened using microbead display technology that utilized emulsion PCR and cell-free protein synthesis. After one round of screening, the binding activities of collected mutants were estimated using flow cytometry and a peptide array. Two of these exhibited improved association rate constants to ang II, compared to the P2 peptide.

Analyses of binding sequences of the PhaR protein of Rhodobacter sphaeroides FJ1

The phaC, phaP, phaR, and phaZ genes are involved in the synthesis, accumulation, and degradation of poly-beta-hydroxybutyrate (PHB). These genes encode the PHB synthase, phasin, regulatory protein, and PHB depolymerase, respectively, and are located in the same locus in the genome of Rhodobacter sphaeroides FJ1, a purple nonsulfur bacterium capable of producing PHB. We have previously found that the PhaR protein binds to the promoter regions of phaP, phaR, and phaZ and represses their expression. In this study, we determined that PhaR binds to an 11-bp palindromic sequence, 5'-CTGCN(3)GCAG-3', located at nucleotides -69 to -59 and -97 to -87 relative to the translation start site of phaP. Substitution of the three spacer nucleotides with any three or four nucleotides in this sequence had no effect on PhaR binding, but all other base deletions or substitutions in this sequence abolished its ability to bind PhaR both in vitro and in vivo. These results suggest that PhaR regulates the expression of phaP in R. sphaeroides FJ1.

Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel

The amplification of millions of single molecules in parallel can be performed on microscopic magnetic beads that are contained in aqueous compartments of an oil-buffer emulsion. These bead-emulsion amplification (BEA) reactions result in beads that are covered by almost-identical copies derived from a single template. The post-amplification analysis is performed using different fluorophore-labeled probes. We have identified BEA reaction conditions that efficiently produce longer amplicons of up to 450 base pairs. These conditions include the use of a Titanium Taq amplification system. Second, we explored alternate fluorophores coupled to probes for post-PCR DNA analysis. We demonstrate that four different Alexa fluorophores can be used simultaneously with extremely low crosstalk. Finally, we developed an allele-specific extension chemistry that is based on Alexa dyes to query individual nucleotides of the amplified material that is both highly efficient and specific.

DNA-binding specificity of the CYS3 transcription factor of Neurospora crassa defined by binding-site selection

The CYS3 transcription factor is a basic region-leucine zipper (bZIP) DNA-binding protein that is essential for the expression of a coordinately regulated group of genes involved in the acquisition and utilization of sulfur in Neurospora crassa. An approach of using binding-site selection from random-sequence oligonucleotides was used to define CYS3-binding specificity. The derived consensus-binding site of ATGGCGCCAT defines a symmetrical sequence (half-site A T G/t G/a C/t) that resembles that of other bZIP proteins such as CREB and C/EBP. By comparison, CYS3 shows a greater range of binding to a central core of varied Pur-Pyr-Pur-Pyr sequences than CREB as determined by gel shift assays. The derived CYS3 consensus binding sequence was further validated by demonstrating in vivo sulfur regulation using a heterologous promoter construct. The CYS3-binding site data will be useful for the genome-wide study of sulfur-regulated genes in N. crassa, which has served as a model fungal sulfur control system.

Autoregulator protein PhaR for biosynthesis of polyhydroxybutyrate [P(3HB)] possibly has two separate domains that bind to the target DNA and P(3HB): Functional mapping of amino acid residues responsible for DNA binding

PhaR from Paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (PhaP) and PhaR itself, both of which are components of polyhydroxyalkanoate (PHA) granules (A. Maehara, S. Taguchi, T. Nishiyama, T. Yamane, and Y. Doi, J. Bacteriol. 184:3992-4002, 2002). PhaR is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, PHA polyester. In this study, by using a quartz crystal microbalance, we obtained direct evidence that PhaR binds to the target DNA and poly[(R)-3-hydroxybutyrate] [P(3HB)], one of the PHAs, at the same time. To identify the PhaR amino acid residues responsible for DNA binding, deletion and PCR-mediated random point mutation experiments were carried out with the gene encoding the PhaR protein. PhaR point mutants with decreased DNA-binding abilities were efficiently screened by an in vivo monitoring assay system coupled with gene expression of green fluorescent protein in Escherichia coli. DNA-binding abilities of the wild-type and mutants of recombinant PhaR expressed in E. coli were evaluated using a gel shift assay and a surface plasmon resonance analysis. These experiments revealed that basic amino acids and a tyrosine in the N-terminal region, which is highly conserved among PhaR homologs, are responsible for DNA binding. However, most of the mutants with decreased DNA-binding abilities were unaffected in their ability to bind P(3HB), strongly suggesting that PhaR has two separate domains capable of binding to the target DNA and P(3HB).