Analysis of interactions between huGATA-3 transcription factor and three GATA regulatory elements of HIV-1 long terminal repeat, by surface plasmon resonance

Electrochemical biosensor based on topological insulator Bi2Se3 tape electrode for HIV-1 DNA detection

A large-size Bi₂Se₃ tape electrode (BTE) was prepared by peeling off a 2 × 1 × 0.5 cm high-quality single crystal. The feasibility of using the flexible BTE as an efficient bioplatform to load Au nanoparticles and probe DNA for HIV-1 DNA electrochemical sensing was explored. Differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) show that the resultant biosensor has a wide linear range from 0.1 fM to 1 pM, a low detection limit of 50 aM, excellent selectivity, reproducibility and stability, and is superior to the pM DNA detection level of Pt-Au, graphene-AuNPs hybrid biosensors. This outstanding performance is attributed to the intrinsic surface state of Bi₂Se₃ topological insulator in facilitating electron transfer. Therefore, BTE electrochemical biosensor platform has great potential in the application for sensitive detection of DNA biomarkers.

CD4+ T Cell Subsets and Pathways to HIV Latency

Latent infection of CD4⁺ T cells is the main barrier to eradicating HIV-1 infection from infected patients. The cellular and molecular mechanisms involved in the establishment and maintenance of latent infection are directly linked to the transcriptional program of the different CD4⁺ T cell subsets targeted by the virus. In this review, we provide an overview of how T cell activation, T cell differentiation into functional subsets, and the mode of initial viral infection influence HIV proviral transcription and entry into latency.

Identification of c-Jun as bcl-2 Transcription Factor in Human Uterine Endometrium

We describe the application of the biomolecular interaction (BIA) technique to detection of the interaction between protein (e.g., c-Jun) and DNA (e.g., two AP-1 motifs from bcl-2 promoter), compared with immunohistochemistry (IHC) of c-Jun. The specific binding assay for the interaction of c-Jun and activating protein-1 (AP-1) motifs was performed using a Biacore 2000 system. Intense immunoreactivity of c-Jun in glandular cells of the human uterine endometrium was observed in the proliferative phase, while c-Jun in stromal cells was expressed throughout the menstrual cycle. In contrast to the IHC of c-Jun, the specific binding of c-Jun to two separate AP-1 motifs in the bcl-2 promoter region was detected only in nuclear extracts of glandular cells, but not in stromal cells, during the proliferative phase. These results indicate that, while transmitting various signals, c-Jun enhances the transcription level of bcl-2, which in turn keeps glandular cells alive and proliferating in normal human endometrium during the proliferative phase. Moreover, the method involving real-time biomolecular interactions such as DNA-protein binding is novel for the study of transcription factors when combined with IHC.

T Cell Transcription Factors and Their Impact on HIV Expression

By targeting CD4⁺ effector T cells, HIV has a dramatic impact on the depletion, expansion and function of the different polarized T cell subsets. The maturation of T cell lineages is in part driven by intrinsic transcription factors that potentially influence how efficiently HIV replicates. In this review, we explore whether transcription factors that are required for polarizing T cells influence HIV replication. In particular, we examine provirus transcription as well as the establishment and maintenance of HIV latency. Furthermore, it is suggested these factors may provide novel cell-specific therapeutic strategies for targeting the HIV latent reservoir.

Regulation of bcl-2 transcription by estrogen receptor-α and c-Jun in human endometrium

The estrogen-estrogen receptor (ER) signaling pathway plays crucial physiologic roles in not only the control of reproduction, but also in the generation of cancer in the breast and uterus. While some ER target genes have been identified containing the estrogen-responsive element (ERE), others are activated eventually by ER via protein-protein interaction without binding to ERE. In a previous study, we identified that the proliferative phase-specific expression of the bcl-2 gene in glandular cells could be regulated by the binding of c-Jun to its motifs in the promoter. Results from our present study indicate that the menstrual cyclic expression of bcl-2 could be controlled by either direct binding of ERα to ERE in the c-Jun promoter or the interaction of ERα with c-Jun that binds to its motifs in the bcl-2 gene. Intriguingly, the transcriptionally active form of c-Jun phosphorylated at Ser63 was identified binding to its motifs in the bcl-2 gene in a menstrual cyclic non-specific manner. Our study revealed a novel mechanism that transcriptionally regulates the expression of bcl-2 in the normal human endometrium.

In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum

Background

Malaria is the most important parasitic disease in the world with approximately two million people dying every year, mostly due to Plasmodium falciparum infection. During its complex life cycle in the Anopheles vector and human host, the parasite requires the coordinated and modulated expression of diverse sets of genes involved in epigenetic, transcriptional and post-transcriptional regulation. However, despite the availability of the complete sequence of the Plasmodium falciparum genome, we are still quite ignorant about Plasmodium mechanisms of transcriptional gene regulation. This is due to the poor prediction of nuclear proteins, cognate DNA motifs and structures involved in transcription.

Results

A comprehensive directory of proteins reported to be potentially involved in Plasmodium transcriptional machinery was built from all in silico reports and databanks. The transcription-associated proteins were clustered in three main sets of factors: general transcription factors, chromatin-related proteins (structuring, remodelling and histone modifying enzymes), and specific transcription factors. Only a few of these factors have been molecularly analysed. Furthermore, from transcriptome and proteome data we modelled expression patterns of transcripts and corresponding proteins during the intra-erythrocytic cycle. Finally, an interactome of these proteins based either on in silico or on 2-yeast-hybrid experimental approaches is discussed.

Conclusion

This is the first attempt to build a comprehensive directory of potential transcription-associated proteins in Plasmodium. In addition, all complete transcriptome, proteome and interactome raw data were re-analysed, compared and discussed for a better comprehension of the complex biological processes of Plasmodium falciparum transcriptional regulation during the erythrocytic development.

Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy

Quantitative, real-time measurement of kinetics of sequence-specific binding of DNA-binding proteins to double-stranded DNA (dsDNA) immobilized in a 10 x 12 array on a planar gold surface is demonstrated using surface plasmon resonance (SPR) microscopy. This binding of the yeast transcription factor Gal4 to a 120-spot dsDNA array made with alternating 200-microm spots of its dsDNA operator sequence and an unrelated DNA sequence proves that this method could be used to simultaneously monitor the kinetics of binding of proteins to 120 different dsDNA sequences with a sensitivity to approximately 0.5 pg (<2 x 10(7) molecules) of bound protein in each array spot at a time resolution of 1 s. The method is label free and also allows absolute quantitative determination of the binding stoichiometry (i.e., the number of proteins bound per dsDNA) at each time. The dsDNA array was fabricated using a robotic microspotting system to deliver nanoliter droplets of biotinylated dsDNA solutions onto a streptavidin linker layer immobilized with biotinylated alkylthiols on a thin gold film. Simultaneous monitoring of binding to the many array elements allows the use of reference spots (i.e., array elements with unrelated dsDNA sequences) to correct the signal for nonspecific protein-DNA binding and changes in bulk refractive index of the solutions in the SPR microscope's flow cell. This allows high-throughput analyses of the kinetics and equilibrium of protein-dsDNA binding.

Evaluation of MafG interaction with Maf recognition element arrays by surface plasmon resonance imaging technique

Specific interactions between transcription factors and cis-acting DNA sequence motifs are primary events for the transcriptional regulation. Many regulatory elements appear to diverge from the most optimal recognition sequences. To evaluate affinities of a transcription factor to various suboptimal sequences, we have developed a new detection method based on the surface plasmon resonance (SPR) imaging technique. Transcription factor MafG and its recognition sequence MARE (Maf recognition elements) were adopted to evaluate the new method. We modified DNA immobilization procedure on to the gold chip, so that a double-stranded DNA array was successfully fabricated. We further found that a hydrophilic flexible spacer composed of the poly (ethylene glycol) moiety between DNA and alkanethiol self-assembled monolayers on the surface is effective for preventing nonspecific adsorption and facilitating specific binding of MafG. Multiple interaction profiles between MafG and six of MARE-related sequences were observed by the SPR imaging technique. The kinetic values obtained by SPR imaging showed very good correlation with those obtained from electrophoretic gel mobility shift assays, although absolute values were deviated from each other. These results demonstrate that the double-stranded DNA array fabricated with the modified multistep procedure can be applied for the comprehensive analysis of the transcription factor-DNA interaction.

Spying on HIV with SPR

The application of surface plasmon resonance (SPR)-based optical biosensors has contributed extensively to our understanding of functional aspects of HIV. SPR biosensors allow the analysis of real-time interactions of any biomolecule, be it protein, nucleic acid, lipid, carbohydrate or small molecule, without the need for intrinsic or extrinsic probes. As such, the technology has been used to analyze molecular interactions associated with every aspect of the viral life cycle, from basic studies of binding events occurring during docking, replication, budding and maturation to applied research related to vaccine and inhibitory drug development. Along the way, SPR biosensors have provided a unique and detailed view into the inner workings of HIV.

Biospecific interaction analysis: a tool for drug discovery and development

The recent development of surface plasmon resonance (SPR)-based biosensor technologies for biospecific interaction analysis (BIA) enables the monitoring of a variety of molecular reactions in real-time. The biomolecular interactions occur at the surface of a flow cell of a sensor chip between a ligand immobilized on the surface and an injected analyte. SPR-based BIA offers many advantages over most of the other methodologies available for the study of biomolecular interactions, including full automation, no requirement for labeling, and the availability of a large variety of activated sensor chips that allow immobilization of DNA, RNA, proteins, peptides and cells. The assay is rapid and requires only small quantitities of both ligand and analyte in order to obtain informative results. In addition, the sensor chip can be re-used many times, leading to low running costs. Aside from the analysis of all possible combinations of peptide, protein, DNA and RNA interactions, this technology can also be used for screening of monoclonal antibodies and epitope mapping, analysis of interactions between low molecular weight compounds and proteins or nucleic acids, interactions between cells and ligands, and real-time monitoring of gene expression. Applications of SPR-based BIA in medicine include the molecular diagnosis of viral infections and genetic diseases caused by point mutations. Future perspectives include the combinations of SPR-based BIA with mass spectrometry, the use of biosensors in proteomics, and the application of this technology to design and develop efficient drug delivery systems.

Contributions of mass spectrometry in the study of nucleic acid-binding proteins and of nucleic acid-protein interactions

Nucleic-acid-protein (NA-P) interactions play essential roles in a variety of biological processes-gene expression regulation, DNA repair, chromatin structure regulation, transcription regulation, RNA processing, and translation-to cite only a few. Such biological processes involve a broad spectrum of NA-P interactions as well as protein-protein (P-P) interactions. These interactions are dynamic, in terms of the chemical composition of the complexes involved and in terms of their mere existence, which may be restricted to a given cell-cycle phase. In this review, the contributions of mass spectrometry (MS) to the deciphering of these intricate networked interactions are described along with the numerous applications in which it has proven useful. Such applications include, for example, the identification of the partners involved in NA-P or P-P complexes, the identification of post-translational modifications that (may) regulate such complexes' activities, or even the precise molecular mapping of the interaction sites in the NA-P complex. From a biological standpoint, we felt that it was worth the reader's time to be as informative as possible about the functional significance of the analytical methods reviewed herein. From a technical standpoint, because mass spectrometry without proper sample preparation would serve no purpose, each application described in this review is detailed by duly emphasizing the sample preparation-whenever this step is considered innovative-that led to significant analytical achievements.

An optical method for the detection of oxidative stress using protein-RNA interaction

The cytosolic 4Fe-4S protein aconitase can be converted under the influence of reactive oxygen species into an iron-regulatory protein (IRP1). Therefore, the IRP1 level is considered as an indirect marker of oxidative stress. An experimental approach is presented here to detect the concentration of this marker protein by surface plasmon resonance. The optical method exploits the natural binding affinity of IRP1 to an iron-responsive element (IRE) which was in vitro transcribed with a linker sequence and subsequently immobilized on a BIACORE sensor chip. The detection was found to be reproducible and sensitive in the range 20-200 nM IRP. Conditions of the binding process, such as pH and thiol concentration, were characterized. Feasibility of the method to detect and quantify IRP1 in physiological media was demonstrated.

Interaction of the human NF-kappaB p52 transcription factor with DNA-PNA hybrids mimicking the NF-kappaB binding sites of the human immunodeficiency virus type 1 promoter

We determined whether peptide nucleic acids (PNAs) are able to interact with NF-kappaB p52 transcription factor. The binding of NF-kappaB p52 to DNA-DNA, DNA-PNA, PNA-DNA, and PNA-PNA hybrid molecules carrying the NF-kappaB binding sites of human immunodeficiency type 1 long terminal repeat was studied by (i) biospecific interaction analysis (BIA) using surface plasmon resonance technology, (ii) electrophoretic mobility shift, (iii) DNase I footprinting, and (iv) UV cross-linking assays. Our results demonstrate that NF-kappaB p52 does not efficiently bind to PNA-PNA hybrids. However, a DNA-PNA hybrid molecule was found to be recognized by NF-kappaB p52, although the molecular complexes generated exhibited low stability. From the theoretical point of view, our results suggest that binding of NF-kappaB p52 protein to target DNA motifs is mainly due to contacts with bases; interactions with the DNA backbone are, however, important for stabilization of the protein-DNA complex. From the practical point of view, our results suggest that DNA-PNA hybrid can be recognized by NF-kappaB p52 protein, although with an efficiency lower than DNA-DNA NF-kappaB target molecules; therefore, our results should encourage studies on modified PNAs in order to develop potential agents for the decoy approach in gene therapy.

Real-time study of interactions between a composite DNA regulatory region (HIV-1 LTR NRE) and several transcription factors of nuclear extracts

Here we describe the first real-time study of nuclear protein interaction with a composite DNA regulatory region. We studied the interplay between the three target sites of the negative regulatory element (NRE) of HIV-1 LTR, comprising a noncanonical GATA site overlapping two negative regulatory regions, USF and NFIL-6, and their corresponding transcription factors in nuclear extracts. By bandshift analysis, no GATA binding activity could be detected between LTR NRE and different nuclear extracts, although evidenced by in vitro footprinting. Additionally, the LTR NRE and a USF oligonucleotide showed identical retarded complexes. BIAcore study of these interactions revealed the binding of huGATA-3, as well as USF, to the immobilized LTR NRE oligonucleotide. Competition analyses, performed with GATA, USF, and NFIL-6 oligonucleotides, clearly showed that this regulatory region could bind both huGATA-3 and USF factors. Finally, the presence of USF and huGATA-3 proteins in the complexes formed with LTR NRE was ascertained using specific anti-huGATA-3 and anti-USF2 polyclonal antibodies.

Kinetic analysis of DNA binding by the c-Myb DNA-binding domain using surface plasmon resonance

Kinetics of the interaction of the c-Myb DNA-binding domain (R2R3) with its target DNA have been analyzed by surface plasmon resonance measurements. The association and dissociation rate constants between the standard R2R3, the Cys130 mutant substituted with Ile, and the cognate DNA are 2.3x10(5) M(-1) s(-1) and 2.6x10(-3) s(-1) at pH 7.5 and 20 degrees C, respectively. Kinetic analyses of the binding of the standard R2R3 to the non-cognate DNAs and those of the R2R3 mutant proteins to the cognate DNA showed that the reduction of the binding affinity was mainly due to an increase in the dissociation rate.