DNA-protein interactions: methods for detection and analysis

SbYS1 and SbWRKY72 regulate Cd tolerance and accumulation in sweet sorghum

MAIN CONCLUSION

SbYS1 and its upstream transcription factor SbWRKY72 were involved in Cd tolerance and accumulation and are valuable for developing sweet sorghum germplasm with high-Cd tolerance or accumulation ability through genetic manipulation. Cadmium (Cd) is highly toxic and can severely affect human health. Sweet sorghum, as an energy crop, shows great potential in extracting cadmium from Cd-contaminated soils. However, its molecular mechanisms of Cd-tolerance and -accumulation remain largely unknown. Here, we isolated a YSL family gene SbYS1 from the sweet sorghum genotype with high Cd accumulation ability and the expression of SbYS1 in roots was induced by cadmium. GUS staining experiment exhibited that SbYS1 was expressed in the epidermis and parenchyma tissues of roots. Further subcellular localization analysis suggested that SbYS1 was localized in the endoplasmic reticulum and plasma membrane. Yeast transformed with SbYS1 exhibited a sensitive phenotype compared to the control when exposed to Cd-NA (chelates of cadmium and nicotianamine), indicating that SbYS1 may absorb cadmium in the form of Cd-NA. Arabidopsis overexpressing SbYS1 had a longer root length and accumulated less Cd in roots and shoots. SbWRKY72 bound to the promoter of SbYS1 and negatively regulated the expression of SbYS1. Transgenic Arabidopsis of SbWRKY72 showed higher sensitivity to cadmium and increased cadmium accumulation in roots. Our results provide references for improving the phytoremediation efficiency of sweet sorghum by genetic manipulation in the future.

Nicotiana benthamiana Methanol-Inducible Gene (MIG) 21 Encodes a Nucleolus-Localized Protein That Stimulates Viral Intercellular Transport and Downregulates Nuclear Import

The mechanical damage of plant tissues leads to the activation of methanol production and its release into the atmosphere. The gaseous methanol or vapors emitted by the damaged plant induce resistance in neighboring intact plants to bacterial pathogens but create favorable conditions for viral infection spread. Among the Nicotiana benthamiana methanol-inducible genes (MIGs), most are associated with plant defense and intercellular transport. Here, we characterize NbMIG21, which encodes a 209 aa protein (NbMIG21p) that does not share any homology with annotated proteins. NbMIG21p was demonstrated to contain a nucleolus localization signal (NoLS). Colocalization studies with fibrillarin and coilin, nucleolus and Cajal body marker proteins, revealed that NbMIG21p is distributed among these subnuclear structures. Our results show that recombinant NbMIG21 possesses DNA-binding properties. Similar to a gaseous methanol effect, an increased NbMIG21 expression leads to downregulation of the nuclear import of proteins with nuclear localization signals (NLSs), as was demonstrated with the GFP-NLS model protein. Moreover, upregulated NbMIG21 expression facilitates tobacco mosaic virus (TMV) intercellular transport and reproduction. We identified an NbMIG21 promoter (PrMIG21) and showed that it is methanol sensitive; thus, the induction of NbMIG21 mRNA accumulation occurs at the level of transcription. Our findings suggest that methanol-activated NbMIG21 might participate in creating favorable conditions for viral reproduction and spread.

Harnessing regulatory networks in Actinobacteria for natural product discovery

Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches.

ONE-SENTENCE SUMMARY

This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.

Lambda CI Binding to Related Phage Operator Sequences Validates Alignment Algorithm and Highlights the Importance of Overlooked Bonds

Bacteriophage λ's CI repressor protein controls a genetic switch between the virus's lysogenic and lytic lifecycles, in part, by selectively binding to six different DNA sequences within the phage genome-collectively referred to as operator sites. However, the minimal level of information needed for CI to recognize and specifically bind these six unique-but-related sequences is unclear. In a previous study, we introduced an algorithm that extracts the minimal direct readout information needed for λ-CI to recognize and bind its six binding sites. We further revealed direct readout information shared among three evolutionarily related lambdoid phages: λ-phage, Enterobacteria phage VT2-Sakai, and Stx2 converting phage I, suggesting that the λ-CI protein could bind to the operator sites of these other phages. In this study, we show that λ-CI can indeed bind the other two phages' cognate binding sites as predicted using our algorithm, validating the hypotheses from that paper. We go on to demonstrate the importance of specific hydrogen bond donors and acceptors that are maintained despite changes to the nucleobase itself, and another that has an important role in recognition and binding. This in vitro validation of our algorithm supports its use as a tool to predict alternative binding sites for DNA-binding proteins.

Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations

Sequence-specific protein-DNA interactions are crucial in processes such as DNA organization, gene regulation and DNA replication. Obtaining detailed insights into the recognition mechanisms of protein-DNA complexes through experiments is hampered by a lack of resolution in both space and time. Here, we present a molecular simulation approach to quantify the sequence specificity of protein-DNA complexes, that yields results fast, and is generally applicable to any protein-DNA complex. The approach is based on molecular dynamics simulations in combination with a sophisticated steering potential and results in an estimate of the free energy difference of dissociation. We provide predictions of the nucleotide specific binding affinity of the minor groove binding Histone-like Nucleoid Structuring (H-NS) protein, that are in agreement with experimental data. Furthermore, our approach offers mechanistic insight into the process of dissociation. Applying our approach to the major groove binding ETS domain in complex with three different nucleotide sequences identified the high affinity consensus sequence, quantitatively in agreement with experiments. Our protocol facilitates quantitative prediction of protein-DNA complex stability, while also providing high resolution insights into recognition mechanisms. As such, our simulation approach has the potential to yield detailed and quantitative insights into biological processes involving sequence-specific protein-DNA interactions.

Adaptation of CUT&RUN for use in African trypanosomes

This Cleavage Under Targets and Release Using Nuclease (CUT&RUN) protocol produces genomic occupancy data for a protein of interest in the protozoan parasite Trypanosoma brucei. The data produced is analyzed in a similar way as that produced by ChIP-seq. While we describe the protocol for parasites carrying an epitope tag for the protein of interest, antibodies against the native protein could be used for the same purpose.

AoMedA has a complex regulatory relationship with AoBrlA, AoAbaA, and AoWetA in conidiation, trap formation, and secondary metabolism in the nematode-trapping fungus Arthrobotrys oligospora

The asexual sporulation of filamentous fungi is an important mechanism for their reproduction, survival, and pathogenicity. In Aspergillus and several filamentous fungi, BrlA, AbaA, and WetA are the key elements of a central regulatory pathway controlling conidiation, and MedA is a developmental modifier that regulates temporal expression of central regulatory genes; however, their roles are largely unknown in nematode-trapping (NT) fungi. Arthrobotrys oligospora is a representative NT fungus, which can capture nematodes by producing adhesive networks (traps). Here, we characterized the function of AoMedA and three central developmental regulators (AoBrlA, AoAbaA, and AoWetA) in A. oligospora by gene disruption, phenotypic comparison, and multi-omics analyses, as these regulators are required for conidiation and play divergent roles in mycelial development, trap formation, lipid droplet accumulation, vacuole assembly, and secondary metabolism. A combined analysis of phenotypic traits and transcriptome showed that AoMedA and AoWetA are involved in the regulation of peroxisome, endocytosis, and autophagy. Moreover, yeast one-hybrid analysis showed that AoBrlA can regulate AoMedA, AoAbaA, and AoWetA, whereas AoMedA and AoAbaA can regulate AoWetA. Our results highlight the important roles of AoMedA, AoBrlA, AoAbaA, and AoWetA in conidiation, mycelia development, trap formation, and pathogenicity of A. oligospora and provide a basis for elucidating the relationship between conidiation and trap formation of NT fungi. IMPORTANCE Conidiation is the most common reproductive mode for many filamentous fungi and plays an essential role in the pathogenicity of fungal pathogens. Nematode-trapping (NT) fungi are a special group of filamentous fungi owing to their innate abilities to capture and digest nematodes by producing traps (trapping devices). Sporulation plays an important role in the growth and reproduction of NT fungi, and conidia are the basic components of biocontrol reagents for controlling diseases caused by plant-parasitic nematodes. Arthrobotrys oligospora is a well-known NT fungus and is a routinely used model fungus for probing the interaction between fungi and nematodes. In this study, the functions of four key regulators (AoMedA, AoBrlA, AoAbaA, and AoWetA) involved in conidiation were characterized in A. oligospora. A complex interaction between AoMedA and three central regulators was noted; these regulators are required for conidiation and trap formation and play a pleiotropic role in multiple intracellular activities. Our study first revealed the role of AoMedA and three central regulators in conidiation, trap formation, and pathogenicity of A. oligospora, which contributed to elucidating the regulatory mechanism of conidiation in NT fungi and helped in developing effective reagents for biocontrol of nematodes.

A DNA Pull-Down Assay with Diversity Forms of Competitor for Detecting or Evaluating Protein-DNA Interactions

DNA-protein interactions (DPIs) are critical to all living organisms, particularly in the regulation of gene expression, replication, packing, recombination, and DNA repair, as well as RNA transport and translation. Many laboratory techniques have been developed to study the complex interactions of proteins with DNA, such as chromatin immunoprecipitation (ChIP) assays, DNA electrophoretic mobility shift assay (EMSA), and oligonucleotide pull-down assays. Here we describe an effective approach to identify potential DNA-binding proteins: a pull-down assay using DNA-conjugated beads with a customized competition strategy, which conferred a more effective and efficient approach to determine the interaction between DNA and protein(s), therefore dramatically improving the progress to investigate novel DNA-binding proteins.

Deciphering the pathway-specific regulatory network for production of ten-membered enediyne Tiancimycins in Streptomyces sp. CB03234-S

Background

The anthraquinone-fused 10-membered enediynes (AFEs), represented by tiancimycins (TNMs), possess a unique structural feature and promising potentials as payloads of antitumor antibody–drug conjugates. Despite many efforts, the insufficient yields remain a practical challenge for development of AFEs. Recent studies have suggested a unified basic biosynthetic route for AFEs, those core genes involved in the formation of essential common AFE intermediates, together with multiple regulatory genes, are highly conserved among the reported biosynthetic gene clusters (BGCs) of AFEs. The extreme cytotoxicities of AFEs have compelled hosts to evolve strict regulations to control their productions, but the exact roles of related regulatory genes are still uncertain.

Results

In this study, the genetic validations of five putative regulatory genes present in the BGC of TNMs revealed that only three (tnmR1, tnmR3 and tnmR7) of them were involved in the regulation of TNMs biosynthesis. The bioinformatic analysis also revealed that they represented three major but distinct groups of regulatory genes conserved in all BGCs of AFEs. Further transcriptional analyses suggested that TnmR7 could promote the expressions of core enzymes TnmD/G and TnmN/O/P, while TnmR3 may act as a sensor kinase to work with TnmR1 and form a higher class unconventional orphan two-component regulatory system, which dynamically represses the expressions of TnmR7, core enzymes TnmD/G/J/K1/K2 and auxiliary proteins TnmT2/S2/T1/S1. Therefore, the biosynthesis of TNMs was stringently restricted by this cascade regulatory network at early stage to ensure the normal cell growth, and then partially released at the stationary phase for product accumulation.

Conclusion

The pathway-specific cascade regulatory network consisting with TnmR3/R1 and TnmR7 was deciphered to orchestrate the production of TNMs. And it could be speculated as a common regulatory mechanism for productions of AFEs, which shall provide us new insights in future titer improvement of AFEs and potential dynamic regulatory applications in synthetic biology.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01916-z.

An ELISA-based platform for rapid identification of structure-dependent nucleic acid-protein interactions detects novel DNA triplex interactors

Unusual nucleic acid structures play vital roles as intermediates in many cellular processes and, in the case of peptide nucleic acid (PNA)–mediated triplexes, are leveraged as tools for therapeutic gene editing. However, due to their transient nature, an understanding of the factors that interact with and process dynamic nucleic acid structures remains limited. Here, we developed snapELISA (structure-specific nucleic acid-binding protein ELISA), a rapid high-throughput platform to interrogate and compare up to 2688 parallel nucleic acid structure–protein interactions in vitro. We applied this system to both triplex-forming oligonucleotide–induced DNA triplexes and DNA-bound PNA heterotriplexes to describe the identification of previously known and novel interactors for both structures. For PNA heterotriplex recognition analyses, snapELISA identified factors implicated in nucleotide excision repair (XPA, XPC), single-strand annealing repair (RAD52), and recombination intermediate structure binding (TOP3A, BLM, MUS81). We went on to validate selected factor localization to genome-targeted PNA structures within clinically relevant loci in human cells. Surprisingly, these results demonstrated XRCC5 localization to PNA triplex-forming sites in the genome, suggesting the presence of a double-strand break intermediate. These results describe a powerful comparative approach for identifying structure-specific nucleic acid interactions and expand our understanding of the mechanisms of triplex structure recognition and repair.

Whole-cell FRET monitoring of transcription factor activities enables functional annotation of signal transduction systems in living bacteria

Bacteria adapt to their constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor TF–promoter interactions in situ in living bacteria are lacking. Herein, we developed a whole-cell TF–promoter binding assay based on the intermolecular FRET between an unnatural amino acid, l-(7-hydroxycoumarin-4-yl) ethylglycine, which labels TFs with bright fluorescence through genetic encoding (donor fluorophore) and the live cell nucleic acid stain SYTO 9 (acceptor fluorophore). We show that this new FRET pair monitors the intricate TF–promoter interactions elicited by various types of signal transduction systems, including one-component (CueR) and two-component systems (BasSR and PhoPQ), in bacteria with high specificity and sensitivity. We demonstrate that robust CouA incorporation and FRET occurrence is achieved in all these regulatory systems based on either the crystal structures of TFs or their simulated structures, if 3D structures of the TFs were unavailable. Furthermore, using CueR and PhoPQ systems as models, we demonstrate that the whole-cell FRET assay is applicable for the identification and validation of complex regulatory circuit and novel modulators of regulatory systems of interest. Finally, we show that the FRET system is applicable for single-cell analysis and monitoring TF activities in Escherichia coli colonizing a Caenorhabditis elegans host. In conclusion, we established a tractable and sensitive TF–promoter binding assay, which not only complements currently available approaches for DNA–protein interactions but also provides novel opportunities for functional annotation of bacterial signal transduction systems and studies of the bacteria–host interface.

Exploring molecular biology in sequence space: The road to next-generation single-molecule biophysics

Next-generation sequencing techniques have led to a new quantitative dimension in the biological sciences. In particular, integrating sequencing techniques with biophysical tools allows sequence-dependent mechanistic studies. Using the millions of DNA clusters that are generated during sequencing to perform high-throughput binding affinity and kinetics measurements enabled the construction of energy landscapes in sequence space, uncovering relationships between sequence, structure, and function. Here, we review the approaches to perform ensemble fluorescence experiments on next-generation sequencing chips for variations of DNA, RNA, and protein sequences. As the next step, we anticipate that these fluorescence experiments will be pushed to the single-molecule level, which can directly uncover kinetics and molecular heterogeneity in an unprecedented high-throughput fashion. Molecular biophysics in sequence space, both at the ensemble and single-molecule level, leads to new mechanistic insights. The wide spectrum of applications in biology and medicine ranges from the fundamental understanding of evolutionary pathways to the development of new therapeutics.

Study of Interaction of the PARP Family DNA-Dependent Proteins with Nucleosomes Containing DNA Intermediates of the Initial Stages of BER Process

Reaction of (ADP-ribosyl)ation catalyzed by DNA-dependent proteins of the poly(ADP-ribose)polymerase (PARP) family, PARP1, PARP2, and PARP3, comprises the cellular response to DNA damage. These proteins are involved in the base excision repair (BER) process. Despite the extensive research, it remains unknown how PARPs are involved in the regulation of the BER process and how the roles are distributed between the DNA-dependent members of the PARP family. Here, we investigated the interaction of the PARP's family DNA-dependent proteins with nucleosome core particles containing DNA intermediates of the initial stages of BER. To do that, the nucleosomes containing damage in the vicinity of one of the DNA duplex blunt ends were reconstituted based on the Widom's Clone 603 DNA sequence. Dissociation constants of the PARP complexes with nucleosomes bearing DNA contained uracil (Native), apurine/apyrimidine site (AP site), or a single-nucleotide gap with 5'-dRp fragment (Gap) were determined. It was shown that the affinity of the proteins for the nucleosomes increased in the row: PARP3<<PARP2<PARP1; whereas the affinity of each protein for the certain damage type increased in the row: Native = AP site < Gap for PARP1 and PARP2, Gap<<<Native = AP site for PARP3. The interaction regions of each PARP protein with nucleosome were also determined by sodium borohydride cross-linking and footprinting assay. Based on the obtained and published data, the involvement pattern of the PARP1, PARP2, and PARP3 into the interaction with nucleosome particles containing DNA intermediates of the BER process was discussed.

Prediction of effector proteins and their implications in pathogenicity of phytopathogenic filamentous fungi: A review

Plant pathogenic fungi encode and secrete effector proteins to promote pathogenesis. In recent years, the important role of effector proteins in fungi and plant host interactions has become increasingly prominent. In this review, the functional characterization and molecular mechanisms by which fungal effector proteins modulate biological processes and suppress the defense of plant hosts are discussed, with an emphasis on cell localization during fungal infection. This paper also provides a comprehensive review of bioinformatic and experimental methods that are currently available for the identification of fungal effector proteins. We additionally summarize the secretion pathways and the methods for verifying the presence effector proteins in plant host cells. For future research, comparative genomic studies of different pathogens with varying life cycles will allow comprehensive and systematic identification of effector proteins. Additionally, functional analysis of effector protein interactions with a wider range of hosts (especially non-model crops) will provide more detailed repertoires of fungal effectors. Identifying effector proteins and verifying their functions will improve our understanding of their role in causing disease and in turn guide future strategies for combatting fungal infections.

Characterization of a Salmonella transcription factor-DNA complex and identification of the inducer by native mass spectrometry

FraR, a transcriptional repressor, was postulated to regulate the metabolism of the Amadori compound fructose-asparagine (F-Asn) in the foodborne pathogen Salmonella enterica. Here, the DNA- and inducer-binding affinities and stoichiometries of FraR were determined and cross-validated by electrophoretic mobility-shift assays (EMSAs) and online buffer exchange coupled to native mass spectrometry (OBE-nMS). We demonstrate the utility of OBE-nMS to characterize protein and protein-DNA complexes that are not amenable to offline exchange into volatile buffers. OBE-nMS complemented EMSAs by revealing that FraR binds to the operator DNA as a dimer and by establishing 6-phosphofructose-aspartate as the inducer that weakens DNA binding by FraR. These results provide insights into how FraR regulates the expression of F-Asn-catabolizing enzymes and add to our understanding of the intricate bacterial circuitry that dictates utilization of diverse nutrients.

CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants

Non-coding DNA variants (NCVs) impact gene expression by altering binding sites for regulatory complexes. New high-throughput methods are needed to characterize the impact of NCVs on regulatory complexes. We developed CASCADE (Customizable Approach to Survey Complex Assembly at DNA Elements), an array-based high-throughput method to profile cofactor (COF) recruitment. CASCADE identifies DNA-bound transcription factor-cofactor (TF-COF) complexes in nuclear extracts and quantifies the impact of NCVs on their binding. We demonstrate CASCADE sensitivity in characterizing condition-specific recruitment of COFs p300 and RBBP5 (MLL subunit) to the CXCL10 promoter in lipopolysaccharide (LPS)-stimulated human macrophages and quantify the impact of all possible NCVs. To demonstrate applicability to NCV screens, we profile TF-COF binding to ~1,700 single-nucleotide polymorphism quantitative trait loci (SNP-QTLs) in human macrophages and identify perturbed ETS domain-containing complexes. CASCADE will facilitate high-throughput testing of molecular mechanisms of NCVs for diverse biological applications.

Bray et al. develop CASCADE, a method to profile transcription factor (TF)-cofactor (COF) complexes binding to DNA. They demonstrate the approach by profiling complex binding across the CXCL10 cytokine promoter and to ~1,700 single-nucleotide polymorphisms (SNPs). They anticipate that CASCADE can be applied to diverse biological systems to examine regulatory complex binding to DNA.

Rapid Biosensing Method for Detecting Protein-DNA Interactions

Identifying and investigating protein-DNA interactions, which play significant roles in many biological processes, is essential for basic and clinical research. Current techniques for identification of protein-DNA interactions are laborious, time-consuming, and suffer from nonspecific binding and limited sensitivity. To overcome these challenges and assess protein-DNA interactions, we use a magnetic modulation biosensing (MMB) system. In MMB, one of the interacting elements (protein or DNA) is immobilized to magnetic beads, and the other is coupled to a fluorescent molecule. Thus, the link between the magnetic bead and the fluorescent molecule is established only when binding occurs, enabling detection of the protein-DNA interaction. Using magnetic forces, the beads are concentrated and manipulated in a periodic motion in and out of a laser beam, producing a detectable oscillating signal. Using MMB, we detected protein-DNA interactions between short GC-rich DNA sequences and both a purified specificity protein 1 (Sp1) and an overexpressed Buttonhead (BTD) protein in a cell lysate. The specificity of the interactions was assessed using mutated DNA sequences and competition experiments. The assays were experimentally compared with commonly used electrophoretic mobility shift assay, which takes approximately 4-72 h. In comparison, the MMB-based assay's turnaround time is ∼2 h, and it provides unambiguous results and quantitative measures of performance. The MMB system uses simple and cheap components, making it an attractive alternative method over current costly and time-consuming techniques for analyzing protein-DNA interactions. Therefore, we anticipate that the MMB-based technique will significantly advance the detection of protein-DNA interactions in biomedical research.

Real-time, single-molecule observation of biomolecular interactions inside nanophotonic zero mode waveguides

Living cells rely on numerous protein-protein, RNA-protein and DNA-protein interactions for processes such as gene expression, biomolecular assembly, protein and RNA degradation. Single-molecule microscopy and spectroscopy are ideal tools for real-time observation and quantification of nucleic acids-protein and protein-protein interactions. One of the major drawbacks of conventional single-molecule imaging methods is low throughput. Methods such as sequencing by synthesis utilizing nanofabrication and single-molecule spectroscopy have brought high throughput into the realm of single-molecule biology. The Pacific Biosciences RS2 sequencer utilizes sequencing by synthesis within nanophotonic zero mode waveguides. A number of years ago this instrument was unlocked by Pacific Biosciences for custom use by researchers allowing them to monitor biological interactions at the single-molecule level with high throughput. In this capability letter we demonstrate the use of the RS2 sequencer for real-time observation of DNA-to-RNA transcription and RNA-protein interactions. We use a relatively complex model-transcription of structured ribosomal RNA fromE. coliand interactions of ribosomal RNA with ribosomal proteins. We also show evidence of observation of transcriptional pausing without the application of an external force (as is required for single-molecule pausing studies using optical traps). Overall, in the unlocked, custom mode, the RS2 sequencer can be used to address a wide variety of biological assembly and interaction questions at the single-molecule level with high throughput. This instrument is available for use at the Center for Integrated Nanotechnologies Gateway located at Los Alamos National Laboratory.

Screening and Identification of Transcription Factors Potentially Regulating Foxl2 Expression in Chlamys farreri Ovary

Foxl2 is an evolutionarily conserved female sex gene, which is specifically expressed in the ovary and mainly involved in oogenesis and ovarian function maintenance. However, little is known about the mechanism that regulates Foxl2 specific expression during the ovary development. In the present study, we constructed the gonadal yeast one-hybrid (Y1H) library of Chlamysfarreri with ovaries and testes at different developmental stages using the Gateway technology. The library capacity was more than 1.36 × 10⁷ CFU, and the length of the inserted fragment was 0.75 Kb~2 Kb, which fully met the demand of yeast library screening. The highly transcriptional activity promoter sequence of C. farreri Foxl2 (Cf-Foxl2) was determined at -1000~-616 bp by dual-luciferase reporter (DLR) assay and was used as bait to screen possible transcription factors from the Y1H library. Eleven candidate factors, including five unannotated factors, were selected based on Y1H as well as their expressional differences between ovaries and testes and were verified for the first time to be involved in the transcriptional regulation of Cf-Foxl2 by RT-qPCR and DLR. Our findings provided valuable data for further studying the specific regulation mechanism of Foxl2 in the ovary.

Separation and Characterization of Protein-DNA Complexes by EMSA and In-Gel Footprinting

In-gel footprinting enables the precise identification of protein binding sites on the DNA after separation of free and protein-bound DNA molecules by gel electrophoresis in native conditions and subsequent digestion by the nuclease activity of the 1,10-phenanthroline-copper ion [(OP)₂-Cu⁺] within the gel matrix. Hence, the technique combines the resolving power of protein-DNA complexes in the electrophoretic mobility shift assay (EMSA) with the precision of target site identification by chemical footprinting. This approach is particularly well suited to characterize distinct molecular assemblies in a mixture of protein-DNA complexes and to identify individual binding sites within composite operators, when the concentration-dependent occupation of binding sites, with a different affinity, results in the generation of complexes with a distinct stoichiometry and migration velocity in gel electrophoresis.

Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors

The basic helix–loop–helix transcription factor (bHLH TF) family is involved in tissue development, cell differentiation, and disease. These factors have transcriptionally positive, negative, and inactive functions by combining dimeric interactions among family members. The best known bHLH TFs are the E-protein homodimers and heterodimers with the tissue-specific TFs or ID proteins. These cooperative and dynamic interactions result in a complex transcriptional network that helps define the cell’s fate. Here, the reported dimeric interactions of 67 vertebrate bHLH TFs with other family members are summarized in tables, including specifications of the experimental techniques that defined the dimers. The compilation of these extensive data underscores homodimers of tissue-specific bHLH TFs as a central part of the bHLH regulatory network, with relevant positive and negative transcriptional regulatory roles. Furthermore, some sequence-specific TFs can also form transcriptionally inactive heterodimers with each other. The function, classification, and developmental role for all vertebrate bHLH TFs in four major classes are detailed.

Optimization and application of silver staining of non-glycosylated and glycosylated proteins and nucleic acids for agarose native gel electrophoresis

Electrophoresis is one of the major techniques to analyze macromolecular structure and interaction. Its capability depends on the sensitivity and specificity of the staining methods. We have here examined silver staining of proteins and nucleic acids separated by agarose native gel electrophoresis. By comparing five commercial kits, we identified Silver Stain Plus from Bio-Rad most adequate, as it provided little background staining and reasonable band staining. One of the disadvantages of the Silver Stain Plus kit is its variable staining of glycoproteins as tested with several model samples, including hen egg white proteins, α1-acid glycoprotein and SARS-CoV-2 Spike protein. One of the advantages of silver staining is its ability to stain nucleic acids as demonstrated here for a model nucleic acid with two kits. It was then used to monitor the removal of nucleic acids from the affinity-purified maltose binding protein and monoclonal antibody. It also worked well on staining proteins on agarose gels prepared in the vertical mode, although preparation of the vertical agarose gels required technological modifications described in this report. With the silver staining method optimized here, it should be possible in the future to analyze biological samples that may be available in limited quantity.

Characterization of the T4 gp32-ssDNA complex by native, cross-linking, and ultraviolet photodissociation mass spectrometry

Protein-DNA interactions play crucial roles in DNA replication across all living organisms. Here, we apply a suite of mass spectrometry (MS) tools to characterize a protein-ssDNA complex, T4 gp32·ssDNA, with results that both support previous studies and simultaneously uncover novel insight into this non-covalent biological complex. Native mass spectrometry of the protein reveals the co-occurrence of Zn-bound monomers and homodimers, while addition of differing lengths of ssDNA generates a variety of protein:ssDNA complex stoichiometries (1 : 1, 2 : 1, 3 : 1), indicating sequential association of gp32 monomers with ssDNA. Ultraviolet photodissociation (UVPD) mass spectrometry allows characterization of the binding site of the ssDNA within the protein monomer via analysis of holo ions, i.e. ssDNA-containing protein fragments, enabling interrogation of disordered regions of the protein which are inaccessible via traditional crystallographic techniques. Finally, two complementary cross-linking (XL) approaches, bottom-up analysis of the crosslinked complexes as well as MS1 analysis of the intact complexes, are used to showcase the absence of ssDNA binding with the intact cross-linked homodimer and to generate two homodimer gp32 model structures which highlight that the homodimer interface overlaps with the monomer ssDNA-binding site. These models suggest that the homodimer may function in a regulatory capacity by controlling the extent of ssDNA binding of the protein monomer. In sum, this work underscores the utility of a multi-faceted mass spectrometry approach for detailed investigation of non-covalent protein-DNA complexes.

Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

Polymerase-mediated synthesis of p-vinylaniline-coupled fluorescent DNA for the sensing of nucleolin protein-c-myc G-quadruplex interactions

In this paper we report the synthesis of two deoxyuridine derivatives (dUCN2, dUPy)-featuring p-vinylaniline-based fluorophores linked through a propargyl unit at the 5' position-that function as molecular rotors. This probing system proved to be useful for the sensing of gene regulation arising from interactions between this G-quadruplex and nucleolin.

A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules

Biological liquid-liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.

Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era

The fields of application of functional proteomics are not limited to the study of protein–protein interactions; they also extend to those involving protein complexes that bind DNA or RNA. These interactions affect fundamental processes such as replication, transcription, and repair in the case of DNA, as well as transport, translation, splicing, and silencing in the case of RNA. Analytical or preparative experimental approaches, both in vivo and in vitro, have been developed to isolate and identify DNA/RNA binding proteins by exploiting the advantage of the affinity shown by these proteins toward a specific oligonucleotide sequence. The present review proposes an overview of the approaches most commonly employed in proteomics applications for the identification of nucleic acid-binding proteins, such as affinity purification (AP) protocols, EMSA, chromatin purification methods, and CRISPR-based chromatin affinity purification, which are generally associated with mass spectrometry methodologies for the unbiased protein identification.

High-Throughput Protein-Nucleic Acid Interaction Assay Based on Protein-Induced Fluorescence Enhancement

Molecular processes involved in gene expression encompass multitudes of interactions between proteins and nucleic acids. Quantitative description of these interactions is crucial for delineating the mechanisms governing transcription, genome duplication, and translation. Here we describe a detailed protocol for the quantitative analysis of protein-nucleic acid interactions based on protein-induced fluorescence enhancement (PIFE). While PIFE has mainly been used in single-molecule studies, we modified its application for bulk measurement of protein-nucleic acid interactions in microwell plates using standard fluorescent plate readers. The microwell plate PIFE assay (mwPIFE) is simple, does not require laborious protein labeling, and is high throughput. These properties predispose mwPIFE to become a method of choice for routine applications that require multiple parallel measurements such as buffer optimization, competition experiments, or screening chemical libraries for binding modulators.

DNB-based on-chip motif finding: A high-throughput method to profile different types of protein-DNA interactions

Here, we report a sensitive DocMF system that uses next-generation sequencing chips to profile protein-DNA interactions. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer adjacent motif (PAM) sequences of different CRISPR systems. DocMF can simultaneously screen both 5' and 3' PAMs with high coverage. For SpCas9, we found noncanonical 5'-NAG-3' (~5%) and 5'-NGA-3' (~1.6%), in addition to its common PAMs, 5'-NGG-3' (~89.9%). More relaxed PAM sequences of two uncharacterized Cas endonucleases, VeCas9 and BvCas12a, were extensively characterized using DocMF. Moreover, we observed that dCas9, a DNA binding protein lacking endonuclease activity, preferably bound to the previously reported 5'-NGG-3' sequence. In summary, our studies demonstrate that DocMF is the first tool with the capacity to exhaustively assay both the binding and the cutting properties of different DNA binding proteins.

Target genes directly regulated by Eha are required for Edwardsiella tarda survival within macrophages

Eha is a virulence regulator in Edwardsiella tarda (E. tarda). The present study examined how Eha regulated its target genes to affect the bacterial survival within the cells. We constructed the reporter a pGEX-4T-ehaflag plasmid expressing Eha tagged at its C terminus with the flag epitope, and introduced the plasmid into an eha mutant ET13 strain, and obtained a Cehaflag strain. The expression and activity of an EhaFlag fusion protein restored the survival of the Cehaflag as the wild type in macrophages by Western blotting and intracellular survival experiments. We used a monoclonal anti-Flag antibody to precipitate EhaFlag-DNA complexes using chromatic immunoprecipitation (ChIP). We then designed primers based on the differentially-expressed genes identified from RNA-sequencing, and identified ten Eha-interacting genes by qPCR. We amplified the promoter regions of the ten genes and the eha gene from ET13 strain by PCR, constructed pBD-P_targetlacZ and pBD-P_ehalacZ plasmids. The eha gene directly and positively regulated these target genes, and be negatively auto-regulated by Eha in E. tarda, as determined by comparing their β-Galactosidase activities. These target genes were distributed in the categories involved in the bacterial growth, movement and resistance to H₂O₂ or acid. We further constructed a ETATCC_RS15225 mutant (△dcuA1), a ETATCC_ RS14855 mutant (△flgK) anda ETATCC_RS07650 mutant (ΔtnaA), and a partial complementary strains of △eha-tnaA and △eha-flgK and the complementary strains of CΔflgK and CΔtnaA. The ETATCC_RS15225 gene probably encoded a transporter protein DcuA1 at outer membrane with SDS-PAGE and RT-PCR. The ETATCC _RS14855 gene probably encoded FlgK protein and affected the bacterial motility. The ETATCC_RS07650 gene encoded Tryptophanase, which affected the bacterial survival within macrophages. With the assistance of these above strains, our results showed that the eha gene was able to regulate the ETATCC_RS15225 gene to express its outer membrane protein DcuA1, the ETATCC _RS14855 gene to control the flagellar motility and the ETATCC_RS07650 to affect the bacterial survival within macrophages. With the combination of other functions of above three genes, our results suggested that Eha directly regulates the target genes to affect E. tarda to survive within the cells.

Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review

Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.

I-Block: a simple Escherichia coli-based assay for studying sequence-specific DNA binding of proteins

We have developed a simple method called I-Block assay, which can detect sequence-specific binding of proteins to DNA in Escherichia coli. The method works by detecting competition between the protein of interest and RNA polymerase for binding to overlapping target sites in a plasmid-borne lacI promoter variant. The assay utilizes two plasmids and an E. coli host strain, from which the gene of the Lac repressor (lacI) has been deleted. One of the plasmids carries the lacI gene with a unique NheI restriction site created in the lacI promoter. The potential recognition sequences of the tested protein are inserted into the NheI site. Introduction of the plasmids into the E. coliΔlacI host represses the constitutive β-galactosidase synthesis of the host bacterium. If the studied protein expressed from a compatible plasmid binds to its target site in the lacI promoter, it will interfere with lacI transcription and lead to increased β-galactosidase activity. The method was tested with two zinc finger proteins, with the lambda phage cI857 repressor, and with CRISPR-dCas9 targeted to the lacI promoter. The I-Block assay was shown to work with standard liquid cultures, with cultures grown in microplate and with colonies on X-gal indicator plates.

Pioneer factors and their in vitro identification methods

Pioneer transcription factors are a special group of transcription factors that can interact with nucleosomal DNA and initiate regulatory events. Their binding to regulatory regions is the first event in gene activation and can occur in silent or heterochromatin regions. Several research groups have endeavored to define pioneer factors and study their binding characteristics using various techniques. In this review, we describe the in vitro methods used to define and characterize pioneer factors, paying particular attention to differences in methodologies and how these differences can affect results.

Directing a rational design of aptamer-based fluorescence anisotropy assay for sensitive detection of immunoglobulin E by site-specific binding study

Mapping aptamer-protein interactions is important for characterization and applications of aptamers against proteins. We describe here probing affinity interactions between aptamer and immunoglobulin E (IgE) with a fluorescence anisotropy (FA) approach using a series of aptamer probes having single fluorescein (FAM) label at individual nucleotide (A, C, T). Studies of binding between IgE and aptamer probes revealed several possible close-contact sites, e.g., T9, T10, T11, T13, C15, and T17 of a 37-nt aptamer with a stem-loop secondary structure. FAM labeling on these sites resulted in much higher FA values (higher than 0.230 for T10, T11, T13 and C15) of aptamer-IgE complexes than the distant sites (e.g., terminals) of aptamer probably because the bound IgE close to these sites significantly restricted local rotation of FAM. Close-contact site labeled aptamer probes with high affinity allowed to develop a more sensitive FA assay for IgE than distant site labeled aptamers. The FA assay using T10-labeled aptamer with a dissociation constant (K_d) about 0.8 nM enabled selective detection of IgE at 20 pM and large FA increase upon IgE addition. We also found A12, C14, A25, and T27 were important for IgE-aptamer binding as FAM labeling at these sites significantly reduced aptamer affinity. FA study showed the loop region of this stem-loop aptamer was crucial for affinity binding, and IgE bound to the loop. This FA method will be helpful for understanding aptamer-protein binding and making a rational design of aptamer affinity assays for proteins.

Integration and Querying of Heterogeneous Omics Semantic Annotations for Biomedical and Biomolecular Knowledge Discovery

Background:

Exploring various functional aspects of a biological cell system has been a focused research trend for last many decades. Biologists, scientists and researchers are continuously striving for unveiling the mysteries of these functional aspects to improve the health standards of life. For getting such understanding, astronomically growing, heterogeneous and geographically dispersed omics data needs to be critically analyzed. Currently, omics data is available in different types and formats through various data access interfaces. Applications which require offline and integrated data encounter a lot of data heterogeneity and global dispersion issues.

Objective:

For facilitating especially such applications, heterogeneous data must be collected, integrated and warehoused in such a loosely coupled way so that each molecular entity can computationally be understood independently or in association with other entities within or across the various cellular aspects.

Methods:

In this paper, we propose an omics data integration schema and its corresponding data warehouse system for integrating, warehousing and presenting heterogeneous and geographically dispersed omics entities according to the cellular functional aspects.

Results & Conclusion:

Such aspect-oriented data integration, warehousing and data access interfacing through graphical search, web services and application programing interfaces make our proposed integrated data schema and warehouse system better and useful than other contemporary ones.

First Biochemical Steps on Bacterial Transposition Pathways

Transposons are found in a wide variety of forms throughout the prokaryotic world where they actively contribute to the adaptive strategies of bacterial communities and hence, to the continuous emergence of new multiresistant pathogens. Contrasting with their biological and societal impact, only a few bacterial transposons have been the subject of detailed molecular studies. In this chapter, we propose a set of reliable biochemical methods as a primary route for studying new transposition mechanisms. These methods include (a) a straightforward approach termed "thermal shift induction" to produce the transposase in a soluble and properly folded configuration prior to its purification, (b) an adaptation of classical electrophoretic mobility shift assays (EMSA) combined to fluorescently labeled DNA substrates to determine the DNA content of different complexes assembled by the transposase, and (c) a highly sensitive "in-gel" DNA footprinting assay to further characterize these complexes at the base pair resolution level. A combination of these approaches was recently applied to decipher the molecular organization of key intermediates in the Tn3-family transposition pathway, a mechanism that has long been refractory to biochemical studies.

Promoter Pull-Down Assay: A Biochemical Screen for DNA-Binding Proteins

Transcription factors are ubiquitous proteins that associate with promoter DNA and regulate gene expression through a variety of mechanisms. Understanding transcriptional control mechanisms requires in-depth investigation of the binding of transcription factors to the promoters they regulate. There are many in vivo and in vitro methods for testing the binding of a known protein to a promoter, such as chromatin immunoprecipitation and electrophoretic mobility shift assays. However, for these experiments, one must have a protein candidate to test and is not able to identify unknown proteins bound to a particular promoter. Thus, the promoter pull-down assay was developed to fill this void. This method uses DNA as bait to capture proteins that bind to a specific promoter, such as transcription factors, from cellular lysates. Coupled with other experiments, the promoter pull-down assay vastly improves the repertoire of methods available for defining regulatory complexes that influence transcription.

PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy

DNA-protein interactions are vital to cellular function, with key roles in the regulation of gene expression and genome maintenance. Atomic force microscopy (AFM) offers the ability to visualize DNA-protein interactions at nanometre resolution in near-physiological buffers, but it requires that the DNA be adhered to the surface of a solid substrate. This presents a problem when working in biologically relevant protein concentrations, where proteins may be present in large excess in solution; much of the biophysically relevant information can therefore be occluded by non-specific protein binding to the underlying substrate. Here we explore the use of PLLx-b-PEGy block copolymers to achieve selective adsorption of DNA on a mica surface for AFM studies. Through varying both the number of lysine and ethylene glycol residues in the block copolymers, we show selective adsorption of DNA on mica that is functionalized with a PLL10-b-PEG113/PLL1000-2000 mixture as viewed by AFM imaging in a solution containing high concentrations of streptavidin. We show - through the use of biotinylated DNA and streptavidin - that this selective adsorption extends to DNA-protein complexes and that DNA-bound streptavidin can be unambiguously distinguished in spite of an excess of unbound streptavidin in solution. Finally, we apply this to the nuclear enzyme PARP1, resolving the binding of individual PARP1 molecules to DNA by in-liquid AFM.

Surface plasmon resonance based analysis of the binding of LYAR protein to the rs368698783 (G>A) polymorphic Aγ-globin gene sequences mutated in β-thalassemia

Recent studies have identified and characterized a novel putative transcriptional repressor site in a 5' untranslated region of the Aγ-globin gene that interacts with the Ly-1 antibody reactive clone (LYAR) protein. LYAR binds the 5'-GGTTAT-3' site of the Aγ-globin gene, and this molecular interaction causes repression of gene transcription. In β-thalassemia patients, a polymorphism has been demonstrated (the rs368698783 G>A polymorphism) within the 5'-GGTTAT-3' LYAR-binding site of the Aγ-globin gene. The major results gathered from surface plasmon resonance based biospecific interaction analysis (SPR-BIA) studies (using crude nuclear extracts, LYAR-enriched lysates, and recombinant LYAR) support the concept that the rs368698783 G>A polymorphism of the Aγ-globin gene attenuates the efficiency of LYAR binding to the LYAR-binding site. This conclusion was fully confirmed by a molecular docking analysis. This might lead to a very important difference in erythroid cells from β-thalassemia patients in respect to basal and induced levels of production of fetal hemoglobin. The novelty of the reported SPR-BIA method is that it allows the characterization and validation of the altered binding of a key nuclear factor (LYAR) to mutated LYAR-binding sites. These results, in addition to theoretical implications, should be considered of interest in applied pharmacology studies as a basis for the screening of drugs able to inhibit LYAR-DNA interactions. This might lead to the identification of molecules facilitating induced increase of γ-globin gene expression and fetal hemoglobin production in erythroid cells, which is associated with possible reduction of the clinical severity of the β-thalassemia phenotype. Graphical abstract.

Transcription factors–DNA interactions in rice: identification and verification

The completion of the rice genome sequence paved the way for rice functional genomics research. Additionally, the functional characterization of transcription factors is currently a popular and crucial objective among researchers. Transcription factors are one of the groups of proteins that bind to either enhancer or promoter regions of genes to regulate expression. On the basis of several typical examples of transcription factor analyses, we herein summarize selected research strategies and methods and introduce their advantages and disadvantages. This review may provide some theoretical and technical guidelines for future investigations of transcription factors, which may be helpful to develop new rice varieties with ideal traits.

DNA-protein interaction: identification, prediction and data analysis

Life in living organisms is dependent on specific and purposeful interaction between other molecules. Such purposeful interactions make the various processes inside the cells and the bodies of living organisms possible. DNA-protein interactions, among all the types of interactions between different molecules, are of considerable importance. Currently, with the development of numerous experimental techniques, diverse methods are convenient for recognition and investigating such interactions. While the traditional experimental techniques to identify DNA-protein complexes are time-consuming and are unsuitable for genome-scale studies, the current high throughput approaches are more efficient in determining such interaction at a large-scale, but they are clearly too costly to be practice for daily applications. Hence, according to the availability of much information related to different biological sequences and clearing different dimensions of conditions in which such interactions are formed, with the developments related to the computer, mathematics, and statistics motivate scientists to develop bioinformatics tools for prediction the interaction site(s). Until now, there has been much progress in this field. In this review, the factors and conditions governing the interaction and the laboratory techniques for examining such interactions are addressed. In addition, developed bioinformatics tools are introduced and compared for this reason and, in the end, several suggestions are offered for the promotion of such tools in prediction with much more precision.

Options and Considerations When Using a Yeast One-Hybrid System

Comprehensive mapping of protein-DNA interactions is essential to uncover the mechanisms involved in gene regulation. However, the data generated has been sparse given the number of regulatory elements and transcription factors (TFs) encoded in the genomes of metazoan organisms. Yeast one-hybrid (Y1H) assays provide a powerful "DNA-centered" method, complementary to "TF-centered" methods such as chromatin immunoprecipitation, to identify the TFs that can bind a DNA sequence of interest. Here, we present different technical variations that should be considered when using a Y1H system, including the type of DNA sequence to test, source of TF clones, as well as types of vectors and screening format. Finally, we discuss limitations of the assay and future challenges.

Versatile Analysis of DNA-Biomolecule Interactions in Solution by Hydrodynamic Separation and Single Molecule Detection

DNA can interact with a wide array of molecules with a range of binding affinities, stoichiometry, and size-scales. We present a sensitive, quantitative, and versatile platform for sensing and evaluating these diverse DNA-biomolecule interactions and DNA conformational changes in free solution. Single molecule free solution hydrodynamic separation utilizes differences in hydrodynamic mobility to separate bound DNA-biomolecule complexes from unbound DNA and determine the associated size change that results from binding. Single molecule detection enables highly quantitative analysis of the fraction of DNA in the bound and unbound state to characterize binding behavior including affinity, stoichiometry, and cooperativity. A stacked injection scheme increases throughput to enable practical analysis of DNA-biomolecule interactions using only picoliters of sample per measurement. To demonstrate analysis of DNA-protein interactions on a local scale, we investigate binding of the E. coli single stranded binding protein to two DNA oligos both individually and in direct competition. We show that stoichiometry and cooperativity is a function of DNA length and verify these differences in binding characteristics through direct competition. To demonstrate analysis of DNA-small molecule interactions and global conformational changes, we also assess DNA condensation with the polyamine spermidine. We use hydrodynamic mobility to evaluate the size of spermidine-condensed DNA and single molecule burst analysis to evaluate DNA packing within the condensed globules relative to free-coiled DNA. This platform thus presents a versatile tool capable of quantitative and sensitive evaluation of diverse biomolecular interactions, complex properties, and binding characteristics.

Estimating RNA Polymerase Protein Binding Sites on λ DNA Using Solid-State Nanopores

In this work, using a silicon nitride nanopore based device, we measure the binding locations of RNA Polymerase (RNAP) on 48.5 kbp (16.5 μm) long λ DNA. To prevent the separation of bound RNAPs from a λ DNA molecule in the high electric field inside a nanopore, we cross-linked RNAP proteins to λ DNA by formaldehyde. We compare the current blockage event data measured with a mixture of λ DNA and RNAP under cross-link conditions with our control samples: RNAP, λ DNA, RNAP, and λ DNA incubated in formaldehyde separately and in a mixture. By analyzing the time durations and amplitudes of current blockage signals of events and their subevents, as well as subevent starting times, we can estimate the binding efficiency and locations of RNAPs on a λ DNA. Our data analysis shows that under the conditions of our experiment with the ratio of 6 to 1 for RNAP to λ DNA molecules, the probability of an RNAP molecule to bind a λ DNA is ∼42%, and that RNAP binding has a main peak at 3.51 μm ± 0.53 μm, most likely corresponding to the two strong promoter regions at 3.48 and 4.43 μm of λ DNA. However, individual RNAP binding sites were not distinguished with this nanopore setup. This work brings out new perspectives and complications to study transcription factor RNAP binding at various positions on very long DNA molecules.

Characterization of an SSB–dT25 complex: structural insights into the S-shaped ssDNA binding conformation

Single-stranded DNA (ssDNA)-binding proteins (SSBs) play an important role in all DNA-dependent cellular processes, such as DNA replication, recombination, repair, and replication restart. The N-terminal domain of SSBs forms an oligonucleotide/oligosaccharide-binding (OB) fold for ssDNA binding. The SSB–dC35 complex structure has revealed how an Escherichia coli SSB (EcSSB) tetramer binds to 65-nucleotide (nt)-long ssDNA, namely, the (SSB)₆₅ binding mode. Knowledge on whether the ssDNA-binding mode for EcSSB is typical for all SSBs or is bacterial strain and length dependent is limited. Here, we studied the ssDNA-binding properties of a Pseudomonas aeruginosa SSB (PaSSB) and investigated its interaction mode through crystallographic analysis. The complex crystal structure containing a PaSSB tetramer with two ssDNA chains was solved at a resolution of 1.91 Å (PDB entry 6IRQ). Results revealed that each bound ssDNA dT25 adopts an S-shaped conformation. This binding mode, as shown by the complex structure of PaSSB, differs significantly from (SSB)₆₅. ssDNA-binding contributions from aromatic residues in PaSSB, except the contribution of Trp54, were not significant. Using electrophoretic mobility shift analysis, we characterized the stoichiometry of PaSSB complexed with a series of ssDNA homopolymers. The minimal length of ssDNA required for PaSSB tetramer binding and the size of the ssDNA-binding site were 25 and 29 nt, respectively. These observations through structure–function analysis suggested that only two OB folds rather than four OB folds in PaSSB are enough for the formation of a stable complex with ssDNA. The PaSSB noninteracting OB folds proposed here may allow sliding via reptation in a dynamic ssDNA binding process.

Single-stranded DNA (ssDNA)-binding proteins (SSBs) play an important role in all DNA-dependent cellular processes, such as DNA replication, recombination, repair, and replication restart.

Electrophoretic Mobility Shift Assay and Dimethyl Sulfate Footprinting for Characterization of G-Quadruplexes and G-Quadruplex-Protein Complexes

DNA G-quadruplexes are globular nucleic acid secondary structures which occur throughout the human genome under physiological conditions. There is accumulating evidence supporting G-quadruplex involvement in a number of important aspects of genome functions, including transcription, replication, and genomic stability, and that protein and enzyme recognition of G-quadruplexes may represent a key event to regulate physiological or pathological pathways. Two important techniques to study G-quadruplexes and their protein interactions are the electrophoretic mobility shift assay (EMSA) and dimethyl sulfate (DMS) footprinting assay. EMSA, one of the most sensitive and robust methods for studying the DNA-protein interactions, can be used to determine the binding parameters and relative affinities of a protein for the G-quadruplex. DMS footprinting is a powerful assay for the initial characterization of G-quadruplexes, which can be used to deduce the guanine bases involved in the formation of G-tetrads under physiological salt conditions. DMS footprinting can also reveal important information in G-quadruplex-protein complexes on protein contacts and regional changes in DNA G-quadruplex upon protein binding. In this paper, we will provide a detailed protocol for the EMSA and DMS footprinting assays for characterization of G-quadruplexes and G-quadruplex-protein complexes. Expected outcomes and references to extensions of the method will be further discussed.

Preparation of Plant Material for Analysis of Protein-Nucleic Acid Interactions by FRET-FLIM

DNA-binding proteins are involved in the dynamic regulation of various cellular processes such as recombination, replication, and transcription. For investigating dynamic assembly and disassembly of molecular complexes in living cells, fluorescence microscopy represents a tremendous tool in biology. A fluorescence resonance energy transfer (FRET) approach coupled to fluorescence lifetime imaging microscopy (FLIM) has been used recently to monitor protein-DNA associations in plant cells. With this approach, the donor fluorophore is a GFP-tagged binding partner expressed in plant cells. A Sytox® Orange treatment converts nuclear nucleic acids to FRET acceptors. A decrease of GFP lifetime is due to FRET between donor and acceptor, indicating close association of the GFP binding partner and Sytox® Orange-stained DNA. In this chapter, we present a step-by-step protocol for the transient expression in N. benthamiana of GFP-tagged proteins and the fixation and permeabilization procedures used for the preparation of plant material aimed at detecting protein-nucleic acid interactions by FRET-FLIM measurements.