Synthesis, characterization, mechanical and magnetic characteristics of Gd3+ /PO4 3 - substituted zircon for application in hard tissue replacements

The study reports on the use of sol-gel technique to yield zircon type [Zr(1-0.1-x) GdxTi0.1 ] [(SiO4 )1-x (PO4 )x ] solid solution. Titanium has been used as a mineralizer to trigger zircon formation while equimolar concentrations of Gd3+ and PO4 3- were added to determine their accommodation limits in the zircon structure. The crystallization of t-ZrO2 as a dominant phase alongside the crystallization of m-ZrO2 and zircon were detected at 1200°C while their further annealing revealed the formation of zircon as a major phase at 1300°C. Heat treatment at 1400°C revealed the formation of zircon-type solid solution [Zr(1-0.1-x) Gdx Ti0.1 ][(SiO4 )1-x (PO4 )x ] comprising the accommodation of 10 mol.% of Gd3+ /PO4 3- at the zircon lattice. Beyond 10 mol.% of Gd3+ /PO4 3- , the crystallization of GdPO4 as a secondary phase is noticed. Structural analysis revealed the expansion of zircon lattice due to the simultaneous occupancy of Gd3+ /PO4 3- for the corresponding Zr4+ /SiO4 4- sites. The mechanical strength of single-phase zircon solid solution was higher in comparison to that of multiphase materials, namely in the presence of GdPO4 formed as a secondary phase in samples with added equimolar Gd3+ /PO4 3- contents beyond 10 mol.%. Nevertheless, the paramagnetic behavior of the samples demonstrated a steady surge as a function of enhanced Gd3+ content.

Enhancing the zircon yield through the addition of calcium phosphates into ZrO2-SiO2 binary systems: synthesis and structural, morphological, mechanical and in vitro analysis

The crystallization of ZrSiO4 is generally accomplished by the addition of mineralizers into ZrO2-SiO2 binary oxides. The current investigation aimed to investigate the effect of adding calcium phosphates into ZrO2-SiO2 binary oxides on the yield of ZrSiO4. The concentration of calcium phosphate additions were varied to obtain ZrSiO4 that fetches improved mechanical and biological properties for application in hard tissue replacements. The findings highlight the significant role of Ca2+ and P5+ in triggering the ZrSiO4 formation via their accommodation at the Zr4+ and Si4+ sites. Especially, calcium phosphate additions trigger the t- → m-ZrO2 transition beyond 1000 °C, which consequently reacts with SiO2 to promote ZrSiO4 formation. Calcium phosphates are accommodated at the lattice sites of ZrSiO4 with a maximum limit of 20 mol%, beyond which the crystallization of β-Ca3(PO4)2 is noticed. The optimum amount of 20 mol% of calcium phosphates displayed a better strength than that of all the investigated specimens. More than 80% of cell viability in MG-63 cells was invariably determined in all the calcium phosphate-added ZrSiO4 systems.

Acetylene containing 2-(2-hydrazinyl)thiazole derivatives: design, synthesis, and in vitro and in silico evaluation of antimycobacterial activity against Mycobacterium tuberculosis

Mycobacterium tuberculosis resistance to commercially available drugs is increasing day by day. To address this issue, various strategies were planned and are being implemented. However, there is a need for new drugs and rapid diagnostic methods. For this endeavour, in this paper, we present the synthesis of acetylene containing 2-(2-hydrazinyl) thiazole derivatives and in vitro evaluation against the H37Rv strain of Mycobacterium tuberculosis. Among the developed 26 acetylene containing 2-(2-hydrazinyl) thiazole derivatives, eight compounds inhibited the growth of Mycobacterium tuberculosis with MIC values ranging from 100 μg ml^-1 to 50 μg ml^-1. The parent acetylene containing thiosemicarbazones showed promising antimycobacterial activity by inhibiting up to 75% of the Mycobacterium at 50 μg ml^-1. In addition, in silico studies were employed to understand the binding mode of all the novel acetylene-containing derivatives against the KasA protein of the Mycobacterium. Interestingly, the KasA protein interactions with the compounds were similar to the interactions of KasA protein with thiolactomycin and rifampicin. Cytotoxicity study results indicate that the compounds tested are non-toxic to human embryonic kidney cells.

The ribosomal protein eL21 interacts with the protein lysine methyltransferase SMYD2 and regulates its steady state levels

The protein lysine methyltransferase, SMYD2 is involved in diverse cellular events by regulating protein functions through lysine methylation. Though several substrate proteins of SMYD2 are well-studied, only a limited number of its interaction partners have been identified and characterized. Here, we performed a yeast two-hybrid screening of SMYD2 and found that the ribosomal protein, eL21 could interact with SMYD2. SMYD2-eL21 interaction in the human cells was confirmed by immunoprecipitation methods. In vitro pull-down assays revealed that SMYD2 interacts with eL21 directly through its SET and MYND domain. Computational mapping, followed by experimental studies identified that Lys81 and Lys83 residues of eL21 are important for the SMYD2-eL21 interaction. Evolutionary analysis showed that these residues might have co-evolved with the emergence of SMYD2. We found that eL21 regulates the steady state levels of SMYD2 by promoting its transcription and inhibiting its proteasomal degradation. Importantly, SMYD2-eL21 interaction plays an important role in regulating cell proliferation and its dysregulation might lead to tumorigenesis. Our findings highlight a novel extra-ribosomal function of eL21 on regulating SMYD2 levels and imply that ribosomal proteins might regulate wide range of cellular functions through protein-protein interactions in addition to their core function in translation.

PRMT3 interacts with ALDH1A1 and regulates gene-expression by inhibiting retinoic acid signaling

Protein arginine methyltransferase 3 (PRMT3) regulates protein functions by introducing asymmetric dimethylation marks at the arginine residues in proteins. However, very little is known about the interaction partners of PRMT3 and their functional outcomes. Using yeast-two hybrid screening, we identified Retinal dehydrogenase 1 (ALDH1A1) as a potential interaction partner of PRMT3 and confirmed this interaction using different methods. ALDH1A1 regulates variety of cellular processes by catalyzing the conversion of retinaldehyde to retinoic acid. By molecular docking and site-directed mutagenesis, we identified the specific residues in the catalytic domain of PRMT3 that facilitate interaction with the C-terminal region of ALDH1A1. PRMT3 inhibits the enzymatic activity of ALDH1A1 and negatively regulates the expression of retinoic acid responsive genes in a methyltransferase activity independent manner. Our findings show that in addition to regulating protein functions by introducing methylation modifications, PRMT3 could also regulate global gene expression through protein-protein interactions.

Here, the authors demonstrate that protein arginine methyltransferase 3 (PRMT3) interacts with and inhibits the retinal dehydrogenase ALDH1A1, negatively regulating the expression of retinoic acid responsive genes. This study shows that PRMT3 affects diverse biological processes not only by globally regulating protein function through methylation but also by regulating gene expression.

The uncharacterized protein FAM47E interacts with PRMT5 and regulates its functions

The uncharacterized protein FAM47E interacts with and stabilizes the protein arginine methyltransferase PRMT5, regulating its epigenetic functions thereby modulating target gene expression.

Protein arginine methyltransferase 5 (PRMT5) symmetrically dimethylates arginine residues in various proteins affecting diverse cellular processes such as transcriptional regulation, splicing, DNA repair, differentiation, and cell cycle. Elevated levels of PRMT5 are observed in several types of cancers and are associated with poor clinical outcomes, making PRMT5 an important diagnostic marker and/or therapeutic target for cancers. Here, using yeast two-hybrid screening, followed by immunoprecipitation and pull-down assays, we identify a previously uncharacterized protein, FAM47E, as an interaction partner of PRMT5. We report that FAM47E regulates steady-state levels of PRMT5 by affecting its stability through inhibition of its proteasomal degradation. Importantly, FAM47E enhances the chromatin association and histone methylation activity of PRMT5. The PRMT5–FAM47E interaction affects the regulation of PRMT5 target genes expression and colony-forming capacity of the cells. Taken together, we identify FAM47E as a protein regulator of PRMT5, which promotes the functions of this versatile enzyme. These findings imply that disruption of PRMT5–FAM47E interaction by small molecules might be an alternative strategy to attenuate the oncogenic function(s) of PRMT5.

2,4-Di-Tert-Butylphenol Isolated From an Endophytic Fungus, Daldinia eschscholtzii, Reduces Virulence and Quorum Sensing in Pseudomonas aeruginosa

Pseudomonas aeruginosa is among the top three gram-negative bacteria according to the WHO’s critical priority list of pathogens against which newer antibiotics are urgently needed and considered a global threat due to multiple drug resistance. This situation demands unconventional antimicrobial strategies such as the inhibition of quorum sensing to alleviate the manifestation of classical resistance mechanisms. Here, we report that 2,4-di-tert-butylphenol (2,4-DBP), isolated from an endophytic fungus, Daldinia eschscholtzii, inhibits the quorum-sensing properties of P. aeruginosa. We have found that treating P. aeruginosa with 2,4-DBP substantially reduced the secretion of virulence factors as well as biofilm, and its associated factors that are controlled by quorum sensing, in a dose-dependent manner. Concomitantly, 2,4-DBP also significantly reduced the expression of quorum sensing-related genes, i.e., lasI, lasR, rhlI, and rhlR significantly. Importantly, 2,4-DBP restricted the adhesion and invasion of P. aeruginosa to the A549 lung alveolar carcinoma cells. In addition, bactericidal assay with 2,4-DBP exhibited synergism with ampicillin to kill P. aeruginosa. Furthermore, our computational studies predicted that 2,4-DBP could bind to the P. aeruginosa quorum-sensing receptors LasR and RhlR. Collectively, these data suggest that 2,4-DBP can be exploited as a standalone drug or in combination with antibiotic(s) as an anti-virulence and anti-biofilm agent to combat the multidrug resistant P. aeruginosa infection.

In situ formation, structural, mechanical and in vitro analysis of ZrO2/ZnFe2O4 composite with assorted composition ratios

The investigation underline the in situ formation of ZrO₂/ZnFe₂O₄ composites and the resultant structural, morphological, mechanical and magnetic properties. The characterization results ensured the crystallization of tetragonal ZrO₂ (t-ZrO₂) and ZnFe₂O₄ phases at 900 °C. Depending on Zn²⁺/Fe³⁺ content, the composite system revealed a gradual increment in the phase yield of ZnFe₂O₄. The significance of monoclinic ZrO₂ (m-ZrO₂) is also evident in all the systems at 900 °C; however, the incremental heat treatment to 1300 °C indicated its corresponding loss, thus indicating the reverse m- → t-ZrO₂ transition. The crystallization of ZnFe₂O₄ as a secondary phase in the t-ZrO₂ matrix is also affirmed from the morphological analysis. Mechanical studies accomplished good uniformity in all the investigated compositions despite the variation in the phase content of ZnFe₂O₄ in composite system. All the t-ZrO₂/ZnFe₂O₄ composites ensured strong ferrimagnetic features and moreover better biocompatibility and non-toxicity characteristics were displayed from in vitro tests.

2,4-Di-Tert-Butylphenol Isolated From an Endophytic Fungus, Daldinia eschscholtzii, Reduces Virulence and Quorum Sensing in Pseudomonas aeruginosa

Pseudomonas aeruginosa is among the top three gram-negative bacteria according to the WHO's critical priority list of pathogens against which newer antibiotics are urgently needed and considered a global threat due to multiple drug resistance. This situation demands unconventional antimicrobial strategies such as the inhibition of quorum sensing to alleviate the manifestation of classical resistance mechanisms. Here, we report that 2,4-di-tert-butylphenol (2,4-DBP), isolated from an endophytic fungus, Daldinia eschscholtzii, inhibits the quorum-sensing properties of P. aeruginosa. We have found that treating P. aeruginosa with 2,4-DBP substantially reduced the secretion of virulence factors as well as biofilm, and its associated factors that are controlled by quorum sensing, in a dose-dependent manner. Concomitantly, 2,4-DBP also significantly reduced the expression of quorum sensing-related genes, i.e., lasI, lasR, rhlI, and rhlR significantly. Importantly, 2,4-DBP restricted the adhesion and invasion of P. aeruginosa to the A549 lung alveolar carcinoma cells. In addition, bactericidal assay with 2,4-DBP exhibited synergism with ampicillin to kill P. aeruginosa. Furthermore, our computational studies predicted that 2,4-DBP could bind to the P. aeruginosa quorum-sensing receptors LasR and RhlR. Collectively, these data suggest that 2,4-DBP can be exploited as a standalone drug or in combination with antibiotic(s) as an anti-virulence and anti-biofilm agent to combat the multidrug resistant P. aeruginosa infection.

Investigation on the structural, mechanical and in vitro biocompatibility features of CaZr4 (PO4 )6 influenced by Zn2+ substitutions

The present study explores the possibility of Zn²⁺ substituted calcium zirconium phosphate [CaZr₄ (PO₄ )₆ ] as a potential replacement for the existing materials in load bearing orthopedic applications. Pure CaZr₄ (PO₄ )₆ ) and wide range of Zn²⁺ substitutions in CaZr₄ (PO₄ )₆ have been synthesized through citrate assisted sol-gel technique. The characterization results confirmed the extraordinary structural stability displayed by CaZr₄ (PO₄ )₆ until 1,550°C. Further, the flexibility of CaZr₄ (PO₄ )₆ lattice to accommodate 40 mol% of Zn²⁺ has been determined. The microstructures of CaZr₄ (PO₄ )₆ and Zn²⁺ substituted CaZr₄ (PO₄ )₆ demonstrated irregular sized grains and cracks alongside the negligence to obtain definite grain boundaries. This has been reflected in the moderate mechanical properties of the investigated specimen; nevertheless, Zn²⁺ substituted CaZr₄ (PO₄ )₆ displayed enhanced mechanical stability. Further, in vitro tests signified the remarkable biocompatibility and alkaline phosphatase activity of Zn²⁺ substituted CaZr₄ (PO₄ )₆ .

DDX49 is an RNA helicase that affects translation by regulating mRNA export and the levels of pre-ribosomal RNA

Among the proteins predicted to be a part of the DExD box RNA helicase family, the functions of DDX49 are unknown. Here, we characterize the enzymatic activities and functions of DDX49 by comparing its properties with the well-studied RNA helicase, DDX39B. We find that DDX49 exhibits a robust ATPase and RNA helicase activity, significantly higher than that of DDX39B. DDX49 is required for the efficient export of poly (A)+ RNA from nucleus in a splicing-independent manner. Furthermore, DDX49 is a resident protein of nucleolus and regulates the steady state levels of pre-ribosomal RNA by regulating its transcription and stability. These dual functions of regulating mRNA export and pre-ribosomal RNA levels enable DDX49 to modulate global translation. Phenotypically, DDX49 promotes proliferation and colony forming potential of cells. Strikingly, DDX49 is significantly elevated in diverse cancer types suggesting that the increased abundance of DDX49 has a role in oncogenic transformation of cells. Taken together, this study shows the physiological role of DDX49 in regulating distinct steps of mRNA and pre-ribosomal RNA metabolism and hence translation and potential pathological role of its dysregulation, especially in cancers.

Structure, luminescence, mechanical and in vitro behavior of zirconia toughened alumina due to terbium substitutions

The significance of Tb³⁺ inclusions at the zirconia toughened alumina (ZTA) structure was explored. The influence of Tb³⁺ content at the crystal structures of ZrO₂ and Al₂O₃ and the resultant optical, mechanical, magnetic and cytotoxicity properties were deliberated. The critical role of Tb³⁺ to attain a structurally stable ZTA until 1500 °C is ensured. Depending on the Tb³⁺ content, either tetragonal zirconia (t-ZrO₂) or cubic zirconia (c-ZrO₂) structures were stabilized while the propensity of Tb³⁺ reaction with Al₂O₃ to yield TbAlO₃ is transpired only after exceeding the occupancy limit in ZrO₂. The green emission and paramagnetic features are imparted by the Tb³⁺ inclusions at the ZTA structure. Dense and pore free microstructures with a direct impact on the improved mechanical features of ZTA is empowered by the presence of Tb³⁺. Further, the results from MTT assay and live/dead cell staining ensured the negligence of Tb³⁺ contained ZTA systems to induce toxicity.

Structural and bio-mineralization features of alumina zirconia composite influenced by the combined Ca2+ and PO43- additions

The structural and bioactivity features of alumina zirconia composite (AZC) due to Ca²⁺ and PO₄^3- additions are demonstrated. An in situ synthetic approach, starting from the solution precursors is devised for the powder synthesis in which the assorted range of Ca²⁺ and PO₄^3- additions were done to the equimolar concentrations of Al³⁺ and Zr⁴⁺ precursors. The results witnessed the unique crystallization of tetragonal zirconia (t-ZrO₂) at 1100 °C while Ca²⁺, PO₄^3- and Al₂O₃ remained in their amorphous state in the system. On further heat treatment, α-Al₂O₃ crystallized at 1200 °C, which enforced t- → m-ZrO₂ transformation while Ca²⁺ and PO₄^3- still retained their amorphous state. The immersion tests in simulated body fluid (SBF) solution validated the enhanced bio-mineralization activity of AZC due to Ca²⁺ and PO₄^3- additions. The results from the indentation tests demonstrated good uniformity in the elastic modulus and hardness data of the investigated specimens. Further, in vitro cell culture tests ascertained the bioactivity of all the AZC compositions.

Organic-to-water dispersible Mn:ZnS–ZnS doped core–shell quantum dots: synthesis, characterization and their application towards optical bioimaging and a turn-off fluorosensor

Dot-in-dot core/shell Mn:ZnS/ZnS QDs as a good fluorescent agent for bioimaging and a turn-off fluorescent probe for detection of heavy metal ions.

DDX39B promotes translation through regulation of pre-ribosomal RNA levels

DDX39B, a DExD RNA helicase, is known to be involved in various cellular processes such as mRNA export, splicing and translation. Previous studies showed that the overexpression of DDX39B promotes the global translation but inhibits the mRNA export in a dominant negative manner. This presents a conundrum as to how DDX39B overexpression would increase the global translation if it inhibits the nuclear export of mRNAs. We resolve this by showing that DDX39B affects the levels of pre-ribosomal RNA by regulating its stability as well as synthesis. Furthermore, DDX39B promotes proliferation and colony forming potential of cells and its levels are significantly elevated in diverse cancer types. Thus, increase in DDX39B enhances global translation and cell proliferation through upregulation of pre-ribosomal RNA. This highlights a possible mechanism by which dysregulation of DDX39B expression could lead to oncogenesis.

Structural, Mechanical, Imaging and in Vitro Evaluation of the Combined Effect of Gd3+ and Dy3+ in the ZrO2-SiO2 Binary System

Mechanical strength and biocompatibility are considered the main prerequisites for materials in total hip replacement or joint prosthesis. Noninvasive surgical procedures are necessary to monitor the performance of a medical device in vivo after implantation. To this aim, simultaneous Gd³⁺ and Dy³⁺ additions to the ZrO₂-SiO₂ binary system were investigated. The results demonstrate the effective role of Gd³⁺ and Dy³⁺ to maintain the structural and mechanical stability of cubic zirconia ( c-ZrO₂) up to 1400 °C, through their occupancy of ZrO₂ lattice sites. A gradual tetragonal to cubic zirconia ( t-ZrO₂ → c-ZrO₂) phase transition is also observed that is dependent on the Gd³⁺ and Dy³⁺ content in the ZrO₂-SiO₂. The crystallization of either ZrSiO₄ or SiO₂ at elevated temperatures is delayed by the enhanced thermal energy consumed by the excess inclusion of Gd³⁺ and Dy³⁺ at c-ZrO₂ lattice. The addition of Gd³⁺ and Dy³⁺ leads to an increase in the density, elastic modulus, hardness, and toughness above that of unmodified ZrO₂-SiO₂. The multimodal imaging contrast enhancement of the Gd³⁺ and Dy³⁺ combinations were revealed through magnetic resonance imaging and computed tomography contrast imaging tests. Biocompatibility of the Gd³⁺ and Dy³⁺ dual-doped ZrO₂-SiO₂ systems was verified through in vitro biological studies.

Identification of protein lysine methylation readers with a yeast three-hybrid approach

BACKGROUND

Protein posttranslational modifications (PTMs) occur broadly in the human proteome, and their biological outcome is often mediated indirectly by reader proteins that specifically bind to modified proteins and trigger downstream effects. Particularly, many lysine methylation sites among histone and nonhistone proteins have been characterized; however, the list of readers associated with them is incomplete.

RESULTS

This study introduces a modified yeast three-hybrid system (Y3H) to screen for methyllysine readers. A lysine methyltransferase is expressed together with its target protein or protein domain functioning as bait, and a human cDNA library serves as prey. Proof of principle was established using H3K9me3 as a bait and known H3K9me3 readers like the chromodomains of CBX1 or MPP8 as prey. We next conducted an unbiased screen using a library composed of human-specific open reading frames. It led to the identification of already known lysine methylation-dependent readers and of novel methyllysine reader candidates, which were further confirmed by co-localization with H3K9me3 in human cell nuclei.

CONCLUSIONS

Our approach introduces a cost-effective method for screening reading domains binding to histone and nonhistone proteins which is not limited by expression levels of the candidate reading proteins. Identification of already known and novel H3K9me3 readers proofs the power of the Y3H assay which will allow for proteome-wide screens of PTM readers.

Size- and defect-controlled anti-oxidant enzyme mimetic and radical scavenging properties of cerium oxide nanoparticles

Improved enzymatic activity and concentration-dependent selective activation of peroxidase and oxidase activity of combustion-synthesized nanoceria.

Iron doped β-Tricalcium phosphate: Synthesis, characterization, hyperthermia effect, biocompatibility and mechanical evaluation

The ability of β-Tricalcium phosphate [β-TCP, β-Ca₃(PO₄)₂] to host iron at its structural lattice and its associated magnetic susceptibility, hyperthermia effect, biocompatibility and mechanical characteristics is investigated. The studies revealed the ability of β-Ca₃(PO₄)₂ to host 5.02mol% of Fe³⁺ at its Ca²⁺(5) site. Excess Fe³⁺ additions led to the formation of trigonal Ca₉Fe(PO₄)₇ and moreover a minor amount of CaFe₃(PO₄)₃O crystallization was also observed. A gradual increment in the iron content at β-Ca₃(PO₄)₂ results in the simultaneous effect of pronounced hyperthermia effect and mechanical stability. However, the presence of CaFe₃(PO₄)₃O contributes for the reduced hyperthermia effect and mechanical stability of iron substituted β-Ca₃(PO₄)₂. Haemolytic tests, cytotoxicity tests and ALP gene expression analysis confirmed the biocompatibility of the investigated systems.

Deposition, structure, physical and invitro characteristics of Ag-doped β-Ca3(PO4)2/chitosan hybrid composite coatings on Titanium metal

Pure and five silver-doped (0-5Ag) β-tricalcium phosphate [β-TCP, β-Ca3(PO4)2]/chitosan composite coatings were deposited on Titanium (Ti) substrates and their properties that are relevant for applications in hard tissue replacements were assessed. Silver, β-TCP and chitosan were combined to profit from their salient and complementary antibacterial and biocompatible features.The β-Ca3(PO4)2 powders were synthesized by co-precipitation. The characterization results confirmed the Ag(+) occupancy at the crystal lattice of β-Ca3(PO4)2. The Ag-dopedβ-Ca3(PO4)2/chitosan composite coatings deposited by electrophoresis showed good antibacterial activity and exhibited negative cytotoxic effects towards the human osteosarcoma cell line MG-63. The morphology of the coatings was observed by SEM and their efficiency against corrosion of metallic substrates was determined through potentiodynamic polarization tests.

The Tudor domain of the PHD finger protein 1 is a dual reader of lysine trimethylation at lysine 36 of histone H3 and lysine 27 of histone variant H3t

PHF1 associates with the Polycomb repressive complex 2 and it was demonstrated to stimulate its H3K27-trimethylation activity. We studied the interaction of the PHF1 Tudor domain with modified histone peptides and found that it recognizes H3K36me3 and H3tK27me3 (on the histone variant H3t) and that it uses the same trimethyllysine binding pocket for the interaction with both peptides. Since both peptide sequences are very different, this result indicates that reading domains can have dual specificities. Sub-nuclear localization studies of full-length PHF1 in human HEK293 cells revealed that it co-localizes with K27me3, but not with K36me3, and that this co-localization depends on the trimethyllysine binding pocket indicating that K27me3 is an in vivo target for the PHF1 Tudor domain. Our data suggest that PHF1 binds to H3tK27me3 in human chromatin, and H3t has a more general role in Polycomb regulation.

Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails

Background

Epigenetic reading domains are involved in the regulation of gene expression and chromatin state by interacting with histones in a post-translational modification specific manner. A detailed knowledge of the target modifications of reading domains, including enhancing and inhibiting secondary modifications, will lead to a better understanding of the biological signaling processes mediated by reading domains.

Results

We describe the application of Celluspots peptide arrays which contain 384 histone peptides carrying 59 post translational modifications in different combinations as an inexpensive, reliable and fast method for initial screening for specific interactions of reading domains with modified histone peptides. To validate the method, we tested the binding specificities of seven known epigenetic reading domains on Celluspots peptide arrays, viz. the HP1ß and MPP8 Chromo domains, JMJD2A and 53BP1 Tudor domains, Dnmt3a PWWP domain, Rag2 PHD domain and BRD2 Bromo domain. In general, the binding results agreed with literature data with respect to the primary specificity of the reading domains, but in almost all cases we obtained additional new information concerning the influence of secondary modifications surrounding the target modification.

Conclusions

We conclude that Celluspots peptide arrays are powerful screening tools for studying the specificity of putative reading domains binding to modified histone peptides.

The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9

Mutations in the ATRX protein are associated with the alpha-thalassemia and mental retardation X-linked syndrome (ATR-X). Almost half of the disease-causing mutations occur in its ATRX-Dnmt3-Dnmt3L (ADD) domain. By employing peptide arrays, chromatin pull-down and peptide binding assays, we show specific binding of the ADD domain to H3 histone tail peptides containing H3K9me3. Peptide binding was disrupted by the presence of the H3K4me3 and H3K4me2 modification marks indicating that the ATRX-ADD domain has a combined readout of these two important marks (absence of H3K4me2 and H3K4me3 and presence of H3K9me3). Disease-causing mutations reduced ATRX-ADD binding to H3 tail peptides. ATRX variants, which fail in the H3K9me3 interaction, show a loss of heterochromatic localization in cells, which indicates the chromatin targeting function of the ADD domain of ATRX. Disruption of H3K9me3 binding may be a general pathogenicity pathway of ATRX mutations in the ADD domain which may explain the clustering of disease mutations in this part of the ATRX protein.

Detailed specificity analysis of antibodies binding to modified histone tails with peptide arrays

Chromatin structure is greatly influenced by histone tail post-translational modifications (PTM), which also play a central role in epigenetic processes. Antibodies against modified histone tails are central research reagents in chromatin biology and molecular epigenetics. We applied Celluspots peptide arrays for the specificity analysis of 36 commercial antibodies from different suppliers which are directed towards modified histone tails. The arrays contained 384 peptides from 8 different regions of the N-terminal tails of histones, viz. H3 1-19, 7-26, 16-35 and 26-45, H4 1-19 and 11-30, H2A 1-19 and H2B 1-19, featuring 59 post-translational modifications in many different combinations. Using various controls we document the reliability of the method. Our analysis revealed previously undocumented details in the specificity profile. Most of the antibodies bound well to the PTM they have been raised for, but some failed. In addition some antibodies showed high cross-reactivity and most antibodies were inhibited by specific additional PTMs close to the primary one. Furthermore, specificity profiles for antibodies directed towards the same modification sometimes were very different. The specificity of antibodies used in epigenetic research is an important issue. We provide a catalog of antibody specificity profiles for 36 widely used commercial histone tail PTM antibodies. Better knowledge about the specificity profiles of antibodies will enable researchers to implement necessary control experiments in biological studies and allow more reliable interpretation of biological experiments using these antibodies.

The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation

The Dnmt3a DNA methyltransferase contains in its N-terminal part a PWWP domain that is involved in chromatin targeting. Here, we have investigated the interaction of the PWWP domain with modified histone tails using peptide arrays and show that it specifically recognizes the histone 3 lysine 36 trimethylation mark. H3K36me3 is known to be a repressive modification correlated with DNA methylation in mammals and heterochromatin in Schizosaccharomyces pombe. These results were confirmed by equilibrium peptide binding studies and pulldown experiments with native histones and purified native nucleosomes. The PWWP-H3K36me3 interaction is important for the subnuclear localization of enhanced yellow fluorescent protein-fused Dnmt3a. Furthermore, the PWWP-H3K36me3 interaction increases the activity of Dnmt3a for methylation of nucleosomal DNA as observed using native nucleosomes isolated from human cells after demethylation of the DNA with 5-aza-2'-deoxycytidine as substrate for methylation with Dnmt3a. These data suggest that the interaction of the PWWP domain with H3K36me3 is involved in targeting of Dnmt3a to chromatin carrying that mark, a model that is in agreement with several studies on the genome-wide distribution of DNA methylation and H3K36me3.

Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail

Using peptide arrays and binding to native histone proteins, we show that the ADD domain of Dnmt3a specifically interacts with the H3 histone 1–19 tail. Binding is disrupted by di- and trimethylation of K4, phosphorylation of T3, S10 or T11 and acetylation of K4. We did not observe binding to the H4 1–19 tail. The ADD domain of Dnmt3b shows the same binding specificity, suggesting that the distinct biological functions of both enzymes are not related to their ADD domains. To establish a functional role of the ADD domain binding to unmodified H3 tails, we analyzed the DNA methylation of in vitro reconstituted chromatin with Dnmt3a2, the Dnmt3a2/Dnmt3L complex, and the catalytic domain of Dnmt3a. All Dnmt3a complexes preferentially methylated linker DNA regions. Chromatin substrates with unmodified H3 tail or with H3K9me3 modification were methylated more efficiently by full-length Dnmt3a and full-length Dnmt3a/3L complexes than chromatin trimethylated at H3K4. In contrast, the catalytic domain of Dnmt3a was not affected by the H3K4me3 modification. These results demonstrate that the binding of the ADD domain to H3 tails unmethylated at K4 leads to the preferential methylation of DNA bound to chromatin with this modification state. Our in vitro results recapitulate DNA methylation patterns observed in genome-wide DNA methylation studies.

A Continuous Protein Methyltransferase (G9a) Assay for Enzyme Activity Measurement and Inhibitor Screening

The authors describe a continuous protein methylation assay using the G9a protein lysine methyltransferase and its substrate protein WIZ (widely interspaced zinc finger motifs). The assay is based on the coupling of the biotinylated substrate protein to streptavidin-coated FlashPlates and the transfer of radioactive methyl groups from the S-adenosyl-L-methionine to the substrate. The reaction progress is monitored continuously by proximity scintillation counting. The assay is very accurate, convenient, well suited for automation, and highly reproducible with standard errors in the range of 5%. Because of few pipetting steps and continuous data readout, it is ideal for high-throughput applications such as screening of inhibitors, testing many enzyme variants, or analyzing differences in methylation rates of different substrates under various conditions. By using this new assay, the IC 50 of AdoHcy and the G9a inhibitor BIX-01294 were determined for methylation of the G9a nonhistone substrate WIZ. ( Journal of Biomolecular Screening 2009:1129-1133)

Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of non-histone proteins

Post translational modification of histone proteins including lysine methylation is an important epigenetic mark, essential for gene regulation and development. Recently, several examples of lysine methylation of non-histone proteins have been discovered suggesting that this is a common post-translational modification for regulation of protein activity. Here, we review assays for the detection of protein methylation based on mass spectrometry, radiolabel and immunological approaches using protein and peptide substrates including application of SPOT peptide arrays. Candidates for new methylation targets of protein methyltransferases can be predicted using the specificity of the enzyme and protein interaction data.

Protein lysine methyltransferase G9a acts on non-histone targets

By methylation of peptide arrays, we determined the specificity profile of the protein methyltransferase G9a. We show that it mostly recognizes an Arg-Lys sequence and that its activity is inhibited by methylation of the arginine residue. Using the specificity profile, we identified new non-histone protein targets of G9a, including CDYL1, WIZ, ACINUS and G9a (automethylation), as well as peptides derived from CSB. We demonstrate potential downstream signaling pathways for methylation of non-histone proteins.

Mapping of protein-protein interaction sites by the 'absence of interference' approach

Protein-protein interactions are critical to most biological processes, and locating protein-protein interfaces on protein structures is an important task in molecular biology. We developed a new experimental strategy called the 'absence of interference' approach to determine surface residues involved in protein-protein interaction of established yeast two-hybrid pairs of interacting proteins. One of the proteins is subjected to high-level randomization by error-prone PCR. The resulting library is selected by yeast two-hybrid system for interacting clones that are isolated and sequenced. The interaction region can be identified by an absence or depletion of mutations. For data analysis and presentation, we developed a Web interface that analyzes the mutational spectrum and displays the mutational frequency on the surface of the structure (or a structural model) of the randomized protein. Additionally, this interface might be of use for the display of mutational distributions determined by other types of random mutagenesis experiments. We applied the approach to map the interface of the catalytic domain of the DNA methyltransferase Dnmt3a with its regulatory factor Dnmt3L. Dnmt3a was randomized with high mutational load. A total of 76 interacting clones were isolated and sequenced, and 648 mutations were identified. The mutational pattern allowed to identify a unique interaction region on the surface of Dnmt3a, which comprises about 500-600 A(2). The results were confirmed by site-directed mutagenesis and structural analysis. The absence-of-interference approach will allow high-throughput mapping of protein interaction sites suitable for functional studies and protein docking.