Similar DNA Binding Properties Research Articles

Synthesis and Characterisation of Platinum(II) Diaminocyclohexane Complexes with Pyridine Derivatives as Anticancer Agents.

Cisplatin-type covalent chemotherapeutics are a cornerstone of modern medicinal oncology. However, these drugs remain encumbered with dose-limiting side effects and are susceptible to innate and acquired resistance. The bulk of platinum anticancer research has focused on Cisplatin and its derivatives. Here, we take inspiration from the design of platinum complexes and ligands used successfully with other metals to create six novel complexes. Herein, the synthesis, characterization, DNA binding affinities, and lipophilicity of a series of non-traditional organometallic Pt(II)-complexes are described. These complexes have a basic [Pt(PL)(AL)]Cl2 molecular formula which incorporates either 2-pyrrolidin-2-ylpyridine, 2-(1H-Imidazol-2-yl)pyridine, or 2-(2-pyridyl)benzimidazole as the PL; the AL is resolved diaminocyclohexane. Precursor [Pt(PL)(Cl)2] complexes were also characterized for comparison. While the cytotoxicity and DNA binding properties of the three precursors were unexceptional, the corresponding [Pt(PL)(AL)]2+ complexes were promising; they exhibited different DNA binding interactions compared with Cisplatin but with similar, if not slightly better, cytotoxicity results. Complexes with 2-pyrrolidin-2-ylpyridine or 2-(2-pyridyl)benzimidazole ligands had similar DNA binding properties to those with 2-(1H-Imidazol-2-yl)pyridine ligands but were not as cytotoxic to all cell lines. The variation in activity between cell lines was remarkable and resulted in significant selectivity indices in MCF10A and MCF-7 breast cancer cell lines, compared with previously described similar Pt(II) complexes such as 56MESS.

PclR is a transcriptional activator of the gene that encodes the pneumococcal collagen-like protein PclA

The Gram-positive bacterium Streptococcus pneumoniae is a major human pathogen that shows high levels of genetic variability. The pneumococcal R6 genome harbours several gene clusters that are not present in all strains of the species. One of these clusters contains two divergent genes, pclA, which encodes a putative surface-exposed protein that contains large regions of collagen-like repeats, and spr1404 (here named pclR). PclA was shown to mediate pneumococcal adherence to host cells in vitro. In this work, we demonstrate that PclR (494 amino acids) is a transcriptional activator. It stimulates transcription of the pclA gene by binding to a specific DNA site upstream of the core promoter. In addition, we show that PclR has common features with the MgaSpn transcriptional regulator (493 amino acids), which is also encoded by the R6 genome. These proteins have high sequence similarity (60.3%), share the same organization of predicted functional domains, and generate multimeric complexes on linear double-stranded DNAs. However, on the PpclA promoter region, MgaSpn binds to a site different from the one recognized by PclR. Our results indicate that PclR and MgaSpn have similar DNA-binding properties but different DNA-binding specificities, pointing to a different regulatory role of both proteins.

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

In eukaryotes, members of transcription factor families often exhibit similar DNA binding properties in vitro, yet orchestrate paralog-specific gene regulatory networks in vivo. The serially homologous first (T1) and third (T3) thoracic legs of Drosophila, which are specified by the Hox proteins Scr and Ubx, respectively, offer a unique opportunity to address this paradox in vivo. Genome-wide analyses using epitope-tagged alleles of both Hox loci in the T1 and T3 leg imaginal discs, the precursors to the adult legs and ventral body regions, show that ~8% of Hox binding is paralog-specific. Binding specificity is mediated by interactions with distinct cofactors in different domains: the Hox cofactor Exd acts in the proximal domain and is necessary for Scr to bind many of its paralog-specific targets, while in the distal leg domain, the homeodomain protein Distal-less (Dll) enhances Scr binding to a different subset of loci. These findings reveal how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene regulatory networks with the help of multiple, context-specific cofactors.

The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins.

Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns− phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.

SOXE neofunctionalization and elaboration of the neural crest during chordate evolution.

During chordate evolution, two genome-wide duplications facilitated acquisition of vertebrate traits, including emergence of neural crest cells (NCCs), in which neofunctionalization of the duplicated genes are thought to have facilitated development of craniofacial structures and the peripheral nervous system. How these duplicated genes evolve and acquire the ability to specify NC and their derivatives are largely unknown. Vertebrate SoxE paralogues, most notably Sox9/10, are essential for NC induction, delamination and lineage specification. In contrast, the basal chordate, amphioxus, has a single SoxE gene and lacks NC-like cells. Here, we test the hypothesis that duplication and divergence of an ancestral SoxE gene may have facilitated elaboration of NC lineages. By using an in vivo expression assay to compare effects of AmphiSoxE and vertebrate Sox9 on NC development, we demonstrate that all SOXE proteins possess similar DNA binding and homodimerization properties and can induce NCCs. However, AmphiSOXE is less efficient than SOX9 in transactivation activity and in the ability to preferentially promote glial over neuronal fate, a difference that lies within the combined properties of amino terminal and transactivation domains. We propose that acquisition of AmphiSoxE expression in the neural plate border led to NCC emergence while duplication and divergence produced advantageous mutations in vertebrate homologues, promoting elaboration of NC traits.

MgaSpn and H-NS: Two Unrelated Global Regulators with Similar DNA-Binding Properties.

Global regulators play an essential role in the adaptation of bacterial cells to specific niches. Bacterial pathogens thriving in the tissues and organs of their eukaryotic hosts are a well-studied example. Some of the proteins that recognize local DNA structures rather than specific nucleotide sequences act as global modulators in many bacteria, both Gram-negative and -positive. To this class of regulators belong the H-NS-like proteins, mainly identified in γ-Proteobacteria, and the MgaSpn-like proteins identified in Firmicutes. H-NS and MgaSpn from Escherichia coli and Streptococcus pneumoniae, respectively, neither have sequence similarity nor share structural domains. Nevertheless, they display common features in their interaction with DNA, namely: (i) they bind to DNA in a non-sequence-specific manner, (ii) they have a preference for intrinsically curved DNA regions, and (iii) they are able to form multimeric complexes on linear DNA. Using DNA fragments from the hemolysin operon regulatory region of the E. coli plasmid pHly152, we show in this work that MgaSpn is able to recognize particular regions on extended H-NS binding sites. Such regions are either located at or flanked by regions of potential bendability. Moreover, we show that the regulatory region of the pneumococcal P1623B promoter, which is recognized by MgaSpn, contains DNA motifs that are recognized by H-NS. These motifs are adjacent to regions of potential bendability. Our results suggest that both regulatory proteins recognize similar structural characteristics of DNA.

Single-molecule study on histone-like nucleoid-structuring protein (H-NS) paralogue in Pseudomonas aeruginosa: MvaU bears DNA organization mode similarities to MvaT.

Pseudomonas aeruginosa contains two distinct members of H-NS family of nucleoid-structuring proteins: MvaT and MvaU. Together, these proteins bind to the same regions of the chromosome and function coordinately in the regulation of hundreds of genes. Due to their structural similarity, they can associate to form heteromeric complexes. These findings left us wondering whether they bear similar DNA binding properties that underlie their gene-silencing functions. Using single-molecule stretching and imaging experiments, we found striking similarities in the DNA organization modes of MvaU compared to the previously studied MvaT. MvaU can form protective nucleoprotein filaments that are insensitive to environmental factors, consistent with its role as a repressor of gene expression. Similar to MvaT, MvaU filament can mediate DNA bridging while excessive MvaU can cause DNA aggregation. The almost identical DNA organization modes of MvaU and MvaT explain their functional redundancy, and raise an interesting question regarding the evolutionary benefits of having multiple H-NS paralogues in the Pseudomonas genus.

Analysis of a bovine herpesvirus 1 protein encoded by an alternatively spliced latency related (LR) RNA that is abundantly expressed in latently infected neurons

The bovine herpes virus 1 (BoHV-1) encoded latency-related RNA (LR-RNA) is abundantly expressed in latently infected sensory neurons. A LR mutant virus with three stop codons at the amino-terminus of ORF2 does not reactivate from latency or replicate efficiently in certain tissues. ORF2 inhibits apoptosis, interacts with Notch1 or Notch3, and interferes with Notch mediated signaling. Alternative splicing of LR-RNA in trigeminal ganglia yields transcripts that have the potential to encode a protein containing most of ORF2 sequences and parts of other coding sequences located within the LR gene. In this study, we determined that an ORF2 protein fused with reading frame B (15d ORF) was more stable in transfected cells. ORF2 and the 15d ORF stimulated neurite formation in mouse neuroblastoma cells, interfered with Notch3 mediated trans-activation, and had similar DNA binding properties. Increased stability of the 15d ORF is predicted to enhance the establishment of latency.

Consensus HIV-1 subtype A integrase and its raltegravir-resistant variants: Design and characterization of the enzymatic properties

Model studies of the subtype B and non-subtype B integrases are still required to compare their susceptibility to antiretroviral drugs, evaluate the significance of resistance mutations and identify the impact of natural polymorphisms on the level of enzymatic reactivity. We have therefore designed the consensus integrase of the HIV-1 subtype A strain circulating in the former Soviet Union territory (FSU-A) and two of its variants with mutations of resistance to the strand transfer inhibitor raltegravir. Their genes were synthesized, and expressed in E coli; corresponding His-tagged proteins were purified using the affinity chromatography. The enzymatic properties of the consensus integrases and their sensitivity to raltegravir were examined in a series of standard in vitro reactions and compared to the properties of the integrase of HIV-1 subtype B strain HXB2. The consensus enzyme demonstrated similar DNA-binding properties, but was significantly more active than HXB-2 integrase in the reactions of DNA cleavage and integration. All integrases were equally susceptible to inhibition by raltegravir and elvitegravir, indicating that the sporadic polymorphisms inherent to the HXB-2 enzyme have little effect on its susceptibility to drugs. Insensitivity of the mutated enzymes to the inhibitors of strand transfer occurred at a cost of a 30-90% loss of the efficacies of both 3'-processing and strand transfer. This is the first study to describe the enzymatic properties of the consensus integrase of HIV-1 clade A and the effects of the resistance mutations when the complex actions of sporadic sequence polymorphisms are excluded.

NR4A Gene Expression Is Dynamically Regulated in the Ventral Tegmental Area Dopamine Neurons and Is Related to Expression of Dopamine Neurotransmission Genes

The NR4A transcription factors NR4A1, NR4A2, and NR4A3 (also known as Nur77, Nurr1, and Nor1, respectively) share similar DNA-binding properties and have been implicated in regulation of dopamine neurotransmission genes. Our current hypothesis is that NR4A gene expression is regulated by dopamine neuron activity and that induction of NR4A genes will increase expression of dopamine neurotransmission genes. Eticlopride and γ-butyrolactone (GBL) were used in wild-type (+/+) and Nurr1-null heterozygous (+/−) mice to determine the mechanism(s) regulating Nur77 and Nurr1 expression. Laser capture microdissection and real-time PCR was used to measure Nurr1 and Nur77 mRNA levels in the ventral tegmental area (VTA). Nur77 expression was significantly elevated 1 h after both GBL (twofold) and eticlopride (fourfold). In contrast, GBL significantly decreased Nurr1 expression in both genotypes, while eticlopride significantly increased Nurr1 expression only in the +/+ mice. In a separate group of mice, haloperidol injection significantly elevated Nur77 and Nor1, but not Nurr1 mRNA in the VTA within 1 h and significantly increased tyrosine hydroxylase (TH) and dopamine transporter (DAT) mRNA expression by 4 h. These data demonstrate that the NR4A genes are dynamically regulated in dopamine neurons with maintenance of Nurr1 expression requiring dopamine neuron activity while both attenuation of dopamine autoreceptors activation and dopamine neuronal activity combining to induce Nur77 expression. Additionally, these data suggest that induction of NR4A genes could regulate TH and DAT expression and ultimately regulate dopamine neurotransmission.

Highly Preferential Linker Histone Binding to Actinomycin D-Treated DNA

ABSTRACTElectromobility-shift assay (EMSA) was applied for studying the competition between the anticancer antibiotic actinomycin D (ACTD) and linker histones H1 and H5 for binding to DNA. ACTD is widely used in the treatment of some malignancies. Its binding to DNA occurs in two steps: initial intercalation between guanine and cytosine bases followed by invading the minor groove of the polynucleotide chain. As a consequence of this structural perturbation of DNA, a strong interference with the binding of important regulatory and functional proteins to DNA may occur. Here we present our recent experimental data obtained in a drug-competition assay between ACTD and linker histones H1 and H5 under the following conditions: i) simultaneous incubation of DNA with the antibiotic and histone; ii) preincubation of DNA with ACTD and subsequent addition of the histone; and iii) preincubation of DNA with histone and subsequent addition of the drug. Surprisingly, linker histones bound more effectively to ACTD-pretreated DNA than to the untreated control. The results obtained with plasmid DNA were confirmed using a series of various native and synthetic DNA fragments bearing different number of antibiotic targets. The same results were obtained with the globular domain of H5, the portion of the linker histone suggested to be most responsible for DNA binding. The data with another nuclear protein with similar DNA-binding properties as linker histones—HMGB1—showed strongly reduced contacts with ACTD-treated DNA compared with the untreated.

Histone H1 Interacts Preferentially with DNA Fragments Containing a Cisplatin- Induced 1,2-Intrastrand Cross-Link

Cisplatin [cis-diamminedichloroplatinum(II) or cis-DDP], but not its stereoisomer transplatin, is suggested to be among the most powerful anticancer agents. It is believed that its therapeutic activity results from its interaction with DNA forming intra- and interstrand crosslinks. During our earlier investigations, we have observed a prominent preference of the linker histone H1 for binding to cis-platinated DNA (containing several different cross-links along the DNA fragment) compared with unmodified or transplatin-modified DNA. This report presents our recent experimental data obtained by band-shift analysis on the binding of H1 to a cisplatin-modified synthetic 34 bp DNA fragment containing a single target d(GG/CC) for 1,2 cis-intra-platination. Results obtained with another nuclear protein with similar DNA-binding properties, HMGB1, are also presented. The experimental data throw light on the precise preference of histone H1 for binding to different types of cisplatin-created cross-links in DNA.

Comparative analysis of Hox downstream genes inDrosophila

Functional diversification of body parts is dependent on the formation of specialized structures along the various body axes. In animals, region-specific morphogenesis along the anteroposterior axis is controlled by a group of conserved transcription factors encoded by the Hox genes. Although it has long been assumed that Hox proteins carry out their function by regulating distinct sets of downstream genes, only a small number of such genes have been found, with very few having direct roles in controlling cellular behavior. We have quantitatively identified hundreds of Hox downstream genes in Drosophila by microarray analysis, and validated many of them by in situ hybridizations on loss- and gain-of-function mutants. One important finding is that Hox proteins, despite their similar DNA-binding properties in vitro, have highly specific effects on the transcriptome in vivo, because expression of many downstream genes respond primarily to a single Hox protein. In addition, a large fraction of downstream genes encodes realizator functions, which directly affect morphogenetic processes, such as orientation and rate of cell divisions, cell-cell adhesion and communication, cell shape and migration, or cell death. Focusing on these realizators, we provide a framework for the morphogenesis of the maxillary segment. As the genomic organization of Hox genes and the interaction of Hox proteins with specific co-factors are conserved in vertebrates and invertebrates, and similar classes of downstream genes are regulated by Hox proteins across the metazoan phylogeny, our findings represent a first step toward a mechanistic understanding of morphological diversification within a species as well as between species.

Linker Histones Do Not Interact with DNA Containing a Single Interstrand Cross-Link Created by Cisplatin

During our earlier investigations we have observed a prominent preference of the linker histone H1 for binding to a cis-platinated DNA (a synthetic fragment with global type of platination in respect to targets for cisplatin) comparing with unmodified and trans-Pt-modified DNA. In the present work we report our recent experimental results on the binding of the linker histones H1 and H5 to a cisplatin-modified synthetic DNA fragment containing a single nucleotide target d(GC/CG) for inter-platination. Surprisingly, no preferential binding of linker histones to cis-inter-platinated DNA was observed by means of the electromobility-shift assay. The same negative results were obtained with a part of the linker histone molecule suggested to be responsible for DNA-binding--its globular domain. Contrary, the data with another nuclear protein with similar DNA-binding properties as linker histones--HMGB1--showed a strong afinity for interaction with DNA containing interstrand cross-links.

Organic Cation Transporters Are Determinants of Oxaliplatin Cytotoxicity

Although the platinum-based anticancer drugs cisplatin, carboplatin, and oxaliplatin have similar DNA-binding properties, only oxaliplatin is active against colorectal tumors. The mechanisms for this tumor specificity of platinum-based compounds are poorly understood but could be related to differences in uptake. This study shows that the human organic cation transporters (OCT) 1 and 2 (SLC22A1 and SLC22A2) markedly increase oxaliplatin, but not cisplatin or carboplatin, accumulation and cytotoxicity in transfected cells, indicating that oxaliplatin is an excellent substrate of these transporters. The cytotoxicity of oxaliplatin was greater than that of cisplatin in six colon cancer cell lines [mean +/- SE of IC(50) in the six cell lines, 3.9 +/- 1.4 micromol/L (oxaliplatin) versus 11 +/- 2.0 micromol/L (cisplatin)] but was reduced by an OCT inhibitor, cimetidine, to a level similar to, or even lower than that of, cisplatin (29 +/- 11 micromol/L for oxaliplatin versus 19 +/- 4.3 micromol/L for cisplatin). Structure-activity studies indicated that organic functionalities on nonleaving groups coordinated to platinum are critical for selective uptake by OCTs. These results indicate that OCT1 and OCT2 are major determinants of the anticancer activity of oxaliplatin and may contribute to its antitumor specificity. They also strongly suggest that expression of OCTs in tumors should be investigated as markers for selecting specific platinum-based therapies in individual patients. The development of new anticancer drugs, specifically targeted to OCTs, represents a novel strategy for targeted drug therapy. The results of the present structure-activity studies indicate specific tactics for realizing this goal.

The C-Terminal Domain of the β Cell Homeodomain Factor Nkx6.1 Enhances Sequence-Selective DNA Binding at the insulin Promoter

The Hox-like factor Nkx6.1 is required for the formation and secretory function of insulin-producing beta cells, and has the capacity to activate or repress the transcription of relevant target genes in a DNA-context dependent manner. A key determinant of transcriptional activity by Nkx6.1 may be its C terminus, which has been suggested to interfere with DNA binding. To determine how the C terminus modulates homeodomain binding, we assessed the nature of Nkx6.1-DNA interactions at the insulin promoter. By quantitative gel shift analysis, we demonstrate that although the C terminus of Nkx6.1 mitigates the affinity of the homeodomain for DNA slightly (about 2-fold), it enhances the selectivity of the homeodomain for TAAT DNA sequences nearly 10-fold. By reporter gene analysis, this selectivity is also functionally preserved in mammalian cells in vivo. Based on deletional and mutational studies, the sequence selectivity imparted by the C terminus appears to be mediated by a stretch of highly conserved residues between amino acids 318 and 338. Strikingly, these residues impart minimal changes to the secondary structure of the unbound protein as assessed by circular dichroism spectroscopy, suggesting that conformational adjustments of the homeodomain that occur upon binding to DNA may play a more important role in sequence selectivity. The C terminus of Nkx6.1 also functions in a modular fashion, as it can confer similar DNA binding properties when fused to the heterologous homeodomain of Pdx-1. Taken together, our data suggest a model whereby the Nkx6.1 C terminus may function in a regulatory manner by imposing specific functional constraints upon the protein. These constraints may serve to modulate the potential of Nkx6.1 to both recognize target genes and regulate their transcription.

DNA Bridging: a Property Shared among H-NS-Like Proteins

The nucleoid-associated protein H-NS is thought to play an essential role in the organization of bacterial chromatin in Escherichia coli. Homologues, often with very low sequence identity, are found in most gram-negative bacteria. Microscopic analysis reveals that, despite limited sequence identity, their structural organization results in similar DNA binding properties.

QRX, a novel homeobox gene, modulates photoreceptor gene expression.

A novel paired-like homeobox gene, designated as Qrx, was identified by a yeast one-hybrid screen using the bovine Rhodopsin promoter Ret-1 DNA regulatory element as bait. Qrx is preferentially expressed in both the outer and inner nuclear layers of the retina. Its homeodomain is nearly identical to that of Rx/Rax, a transcription factor that is essential for eye development, but it shares only limited homology elsewhere. Although Qrx and Rx/Rax show similar DNA binding properties in vitro, the two proteins demonstrate distinct target selectivity and functional behavior in promoter activity assays. QRX synergistically increases the transactivating function of the photoreceptor transcription factors Crx and NRL and it physically interacts with CRX. Qrx is present in the bovine and human genomes, but appears to be absent from the mouse genome. Nonetheless, a 5.8 kb upstream region of human QRX is capable of directing expression in presumptive photoreceptor precursor cells in transgenic mice. These results indicate that Qrx may be involved in modulating photoreceptor gene expression. In addition, the finding of rare heterozygous QRX sequence changes in three individuals with retinal degeneration raises the possibility that QRX may be involved in disease pathogenesis.

Characterization of the chicken L-Maf, MafB and c-Maf in crystallin gene regulation and lens differentiation.

Members of the Maf family, including L-Maf, MafB and c-Maf, are "basic region/leucine zipper" (bZIP) transcription factors. Maf proteins contain a highly conserved acidic transactivation domain (AD), and a bZIP region that mediates DNA-binding activity. The hinge region between AD and bZIP varies considerably in length between different proteins. Recent studies reveal that L-Maf, c-Maf and MafB play key roles in vertebrate lens development. We investigated the transactivation activity of individual factors in culture cells to analyse their specific functions. In transient transfection assays with a reporter gene containing Maf responsive elements, MafB and c-Maf activated higher levels of the reporter gene than L-Maf. However, L-Maf transactivated the alphaA-crystallin promoter as effectively as MafB and c-Maf, and induced the expression of the endogenous delta-crystallin gene more efficiently than the other two proteins. Domain-swapping experiments reveal that the bZIP region of MafB takes part in strong transcriptional activity, while the acidic and hinge regions (AH) of c-Maf collectively serve as a strong transactivation domain. The AH region of L-Maf (but not c-Maf) conferred transactivation activity to induce delta-crystallin gene expression. These results suggest that despite their similar DNA binding properties, L-Maf, MafB and c-Maf regulate different sets of target genes by complex interactions with multiple factors that recognize cis-elements in promoters. The AH region of L-Maf has a distinct role in inducing endogenous delta-crystallin gene.

Identification of bacterial homologues of the Ku DNA repair proteins

Identification of bacterial homologues of the Ku DNA repair proteins