Drop-off-reinitiation at the amino termini of nascent peptides and its regulation by IF3, EF-G, and RRF.

In translation initiation in prokaryotes, IF3 recognizes the interaction between the initiator codon of mRNA and the anticodon of fMet-tRNAini and then relocates the fMet-tRNAini to an active position. Here, we have surveyed 328 codon-anticodon combinations for the preference of IF3. At the first and second base of the codon, only Watson-Crick base pairs are tolerated. At the third base, stronger base pairs, for example, Watson-Crick, are more preferred, but other types of base pairs, for example, G/U wobble, are also tolerated; weaker base pairs are excluded by IF3. When the codon-anticodon combinations are unfavorable for IF3 or the concentration of IF3 is too low to recognize any codon-anticodon combinations, IF3 fails to set the P-site fMet-tRNAini at the active position and causes its drop-off from the ribosome. Thereby, translation reinitiation occurs from the second aminoacyl-tRNA at the A site to yield a truncated peptide lacking the amino-terminal fMet. We refer to this event as the amino-terminal drop-off-reinitiation. We also showed that EF-G and RRF are involved in disassembling such an aberrant ribosome complex bearing inactive fMet-tRNAini Thereby EF-G and RRF are able to exclude unfavorable codon-anticodon combinations with weaker base pairs and alleviate the amino-terminal drop-off-reinitiation.

Structural and Functional Insights into Human Re-initiation Complexes.

After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography. The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.

The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters.

DNA sequence signals in the core promoter, such as the initiator (Inr), direct transcription initiation by RNA polymerase II. Here we show that the human Inr has the consensus of BBCA+1BW at focused promoters in which transcription initiates at a single site or a narrow cluster of sites. The analysis of 7678 focused transcription start sites revealed 40% with a perfect match to the Inr and 16% with a single mismatch outside of the CA+1 core. TATA-like sequences are underrepresented in Inr promoters. This consensus is a key component of the DNA sequence rules that specify transcription initiation in humans.

Finding the start site: redefining the human initiator element.

Transcription by RNA polymerase II (Pol II) is dictated in part by core promoter elements, which are DNA sequences flanking the transcription start site (TSS) that help direct the proper initiation of transcription. Taking advantage of recent advances in genome-wide sequencing approaches, Vo ngoc and colleagues (pp. 6-11) identified transcripts with focused sites of initiation and found that many were transcribed from promoters containing a new consensus sequence for the human initiator (Inr) core promoter element.

Lamotrigine-mediated rescue of RsgA-deficient Escherichia coli reveals another role of IF2 in ribosome biogenesis.

RsgA (small ribosomal subunit, 30S, GTPase), a late-stage biogenesis factor, releases RbfA from 30S-RbfA complex. Escherichia coli ΔrsgA (deleted for rsgA) shows a slow growth phenotype and an increased accumulation of 17S rRNA (precursor of 16S rRNA) and the ribosomal subunits. Here, we show that the rescue of the ΔrsgA strain by multicopy infB (IF2) is enhanced by simultaneous overexpression of initiator tRNA (i-tRNA), suggesting a role of initiation complex formation in growth rescue. The synergistic effect of IF2/i-tRNA is accompanied by increased processing of 17S rRNA (to 16S), and protection of the 16S rRNA 3'-minor domain. Importantly, we show that an IF2-binding anticonvulsant drug, lamotrigine (Ltg), also rescues the ΔrsgA strain growth. The rescue is accompanied by increased processing of 17S rRNA, protection of the 3'-minor domain of 16S rRNA, and increased 70S ribosomes in polysome profiles. However, Ltg becomes inhibitory to the ΔrsgA strain whose growth was already rescued by an L83R mutation in rbfA. Interestingly, like wild-type infB, overproduction of LtgRinfB alleles (having indel mutations in their domain II) also rescues the ΔrsgA strain (independent of Ltg). Our observations suggest the dual role of IF2 in rescuing the ΔrsgA strain. First, together with i-tRNA, IF2 facilitates the final steps of processing of 17S rRNA. Second, a conformer of IF2 functionally compensates for RsgA, albeit poorly, during 30S biogenesis. IMPORTANCE: RsgA is a late-stage ribosome biogenesis factor. Earlier, infB (IF2) was isolated as a multicopy suppressor of the Escherichia coli ΔrsgA strain. How IF2 rescued the strain growth remained unclear. This study reveals that (i) the multicopy infB-mediated growth rescue of E. coli ΔrsgA and the processing of 17S precursor to 16S rRNA in the strain are enhanced upon simultaneous overexpression of initiator tRNA and (ii) a conformer of IF2, whose occurrence increases when IF2 is overproduced or when E. coli ΔrsgA is treated with Ltg (an anticonvulsant drug that binds to domain II of IF2), compensates for the function of RsgA. Thus, this study reveals yet another role of IF2 in ribosome biogenesis.

Mass spectrometry imaging-based assays for aminotransferase activity reveal a broad substrate spectrum for a previously uncharacterized enzyme.

Aminotransferases (ATs) catalyze pyridoxal 5'-phosphate-dependent transamination reactions between amino donor and keto acceptor substrates and play central roles in nitrogen metabolism of all organisms. ATs are involved in the biosynthesis and degradation of both proteinogenic and nonproteinogenic amino acids and also carry out a wide variety of functions in photorespiration, detoxification, and secondary metabolism. Despite the importance of ATs, their functionality is poorly understood as only a small fraction of putative ATs, predicted from DNA sequences, are associated with experimental data. Even for characterized ATs, the full spectrum of substrate specificity, among many potential substrates, has not been explored in most cases. This is largely due to the lack of suitable high-throughput assays that can screen for AT activity and specificity at scale. Here we present a new high-throughput platform for screening AT activity using bioconjugate chemistry and mass spectrometry imaging-based analysis. Detection of AT reaction products is achieved by forming an oxime linkage between the ketone groups of transaminated amino donors and a probe molecule that facilitates mass spectrometry-based analysis using nanostructure-initiator mass spectrometry or MALDI-mass spectrometry. As a proof-of-principle, we applied the newly established method and found that a previously uncharacterized Arabidopsis thaliana tryptophan AT-related protein 1 is a highly promiscuous enzyme that can utilize 13 amino acid donors and three keto acid acceptors. These results demonstrate that this oxime-mass spectrometry imaging AT assay enables high-throughput discovery and comprehensive characterization of AT enzymes, leading to an accurate understanding of the nitrogen metabolic network.

Redundant enhancers in the iab-5 domain cooperatively activate Abd-B in the A5 and A6 abdominal segments of Drosophila.

The Abdominal-B (Abd-B) gene belongs to the bithorax complex and its expression is controlled by four regulatory domains, iab-5, iab-6, iab-7 and iab-8, each of which is thought to be responsible for directing the expression of Abd-B in one of the abdominal segments from A5 to A8. A variety of experiments have supported the idea that BX-C regulatory domains are functionally autonomous and that each domain is both necessary and sufficient to orchestrate the development of the segment they specify. Unexpectedly, we discovered that this model does not always hold. Instead, we find that tissue-specific enhancers located in the iab-5 domain are required for the proper activation of Abd-B not only in A5 but also in A6. Our findings indicate that the functioning of the iab-5 and iab-6 domains in development of the adult cuticle A5 and A6 in males fit better with an additive model, much like that first envisioned by Ed Lewis.

Contributing to the Revolution of Electrolyte Systems via In Situ Polymerization at Different Scales: A Review.

Solid-state batteries have become the most anticipated option for compatibility with high-energy density and safety. In situ polymerization, a novel strategy for the construction of solid-state systems, has extended its application from solid polymer electrolyte systems to other solid-state systems. This review summarizes the application of in situ polymerization strategies in solid-state batteries, which covers the construction of polymer, the formation of the electrolyte system, and the design of the full cell. For the polymer skeleton, multiple components and structures are being chosen. In the construction of solid polymer electrolyte systems, the choice of initiator for in situ polymerization is the focus of this review. New initiators, represented by lithium salts and additives, are the preferred choice because of their ability to play more diverse roles, while the coordination with other components can also improve the electrical properties of the system and introduce functionalities. In the construction of entire solid-state battery systems, the application of in situ polymerization to structure construction, interface construction, and the use of separators with multiplex functions has brought more possibilities for the development of various solid-state systems and even the perpetuation of liquid electrolytes.

A Tough Hydrogel Adhesive for the Repair of Archeological Pottery.

Pottery is the oldest art and plays a landmark role in human civilization. The repair of ceramic relics often uses acrylic resins and cyanoacrylate adhesives. However, existing adhesives often take hours to get cured, and wet adhesion is not possible. We herein propose a redox initiator-triggered hydrogel adhesive, of which robust (∼700 J m-2) and wet adhesion with potsherds can be achieved within a few seconds. The high toughness lies in the self-limited delocalized rupture of the porous interface, and the wet adhesion is due to the hydrophilic precursor and its free radical polymerization. The hydrogel adhesive also exhibits high aging resistance for stable preservation of ∼400 annuals. We have applied the adhesive to the restoration of artifacts excavated from Yinxu, Anyang (∼1300 BC) and the Xia Jiao Shan site (∼4000 BC, Neolithic), and the adhesive is expected to be extended to applications beyond archeology.

Identification and characterization of two novel noncoding tyrosinase (TYR) gene variants leading to oculocutaneous albinism type 1.

Oculocutaneous albinism type 1 (OCA1), resulting from pathogenic variants in the tyrosinase (TYR) gene, refers to a group of phenotypically heterogeneous autosomal recessive disorders characterized by a partial or a complete absence of pigment in the skin/hair and is also associated with common developmental eye defects. In this study, we identified two novel compound heterozygous TYR variants from a Chinese hypopigmentary patient by whole-exome sequencing. Specifically, the two variants were c.-89T>G, located at the core of the initiator E-box (Inr E-box) of the TYR promoter, and p.S16Y (c.47C>A), located within the signal sequence. We performed both in silico analysis and experimental validation and verified these mutations as OCA1 variants that caused either impaired or complete loss of function of TYR. Mechanistically, the Inr E-box variant dampened TYR binding to microphthalmia-associated transcription factor, a master transcriptional regulator of the melanocyte development, whereas the S16Y variant contributed to endoplasmic reticulum retention, a common and principal cause of impaired TYR activity. Interestingly, we found that the Inr E-box variant creates novel protospacer adjacent motif sites, recognized by nucleases SpCas9 and SaCas9-KKH, respectively, without compromising the functional TYR coding sequence. We further used allele-specific genomic editing by CRISPR activation to specifically target the variant promoter and successfully activated its downstream gene expression, which could lead to potential therapeutic benefits. In conclusion, this study expands the spectrum of TYR variants, especially those within the promoter and noncoding regions, which can facilitate genetic counseling and clinical diagnosis of OCA1.

Quantitative Analysis of The High-Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase.

Kelp is an abundant, farmable biomass-containing laminarin and alginate as major polysaccharides, providing an excellent model substrate to study their deconstruction by simple enzyme mixtures. Our previous study showed strong reactivity of the glycoside hydrolase family 55 during hydrolysis of purified laminarin, raising the question of its reactivity with intact kelp. In this study, we determined that a combination of a single glycoside hydrolase family 55 ß-1,3-exoglucanase with a broad-specificity alginate lyase from the polysaccharide lyase family 18 gives efficient hydrolysis of untreated kelp to a mixture of simple sugars, that is, glucose, gentiobiose, mannitol-end glucose, and mannuronic and guluronic acids and their soluble oligomers. Quantitative assignments from nanostructure initiator mass spectrometry (NIMS) and 2D HSQC NMR spectroscopy and analysis of the reaction time-course are provided. The data suggest that binary combinations of enzymes targeted to the unique polysaccharide composition of marine biomass are sufficient to deconstruct kelp into soluble sugars for microbial fermentation.

Exogenous delivery of dsRNA for management of mungbean yellow mosaic virus on blackgram.

MAIN CONCLUSION: Exogenous application of dsRNA molecules targeting MYMV genes offers a promising approach to effectively mitigate yellow mosaic disease in blackgram, demonstrating potential for sustainable plant viral disease management. The exogenous application of double-stranded RNA (dsRNA) molecules to control plant viral diseases is gaining traction due to its advantages over conventional methods, such as target specificity, non-polluting nature, and absence of residue formation. Furthermore, this approach does not involve genome modification. In this study, dsRNA molecules targeting the coat protein gene (dsCP) and replication initiator protein gene (dsRep) of mungbean yellow mosaic virus (MYMV) were synthesised using an in vitro transcription method. To evaluate the effectiveness of dsRNA treatment, blackgram plants exhibiting MYMV symptoms at the first trifoliate stage were subjected to exogenous application of dsRNA. Second, third, and fourth trifoliate leaves, which emerged at 7, 15, and 21 days after dsRNA application, respectively, were monitored for MYMV symptoms. Remarkably, a significant reduction in yellow mosaic disease (YMD) symptoms was observed in the newly emerged trifoliate leaves of MYMV-infected blackgram plants after treatment with dsRNA targeting both gene regions. This reduction was evident as a decrease in the intensity of yellow mosaic coverage on the leaf lamina compared to control. dsCP effectively reduced the MYMV titre in the treated plants for up to 15 days. However, dsRep demonstrated greater efficiency in conferring resistance to MYMV at 15 days post-application. These findings were supported by quantitative real-time PCR analysis, where the observed Ct values for DNA extracted from dsRep-treated plants were significantly higher compared to the Ct values of DNA from dsCP-treated plants at 15 days post-application. Similarly, higher viral copy numbers were observed in dsCP-treated plants 15 days after dsRNA treatment, in contrast to plants treated with dsRep.

A common mechanism links Epstein-Barr virus infections and autoimmune diseases.

Epstein-Barr virus (EBV) infection is associated with a variety of the autoimmune diseases. There is apparently no unified model for the role of EBV in autoimmune diseases. In this article, the development of autoimmune diseases is proposed as a simple two-step process: specific autoimmune initiators may cause irreversible changes to genetic materials that increase autoimmune risks, and autoimmune promoters promote autoimmune disease formation once cells are susceptible to autoimmunity. EBV has several types of latencies including type III latency with higher proliferation potential. EBV could serve as autoimmune initiators for some autoimmune diseases. At the same time, EBV may play a promotional role in majority of the autoimmune diseases by repeated replenishment of EBV type III latency cells and inflammatory cytokine productions in persistent stage. The type III latency cells have enhanced capacity as antigen-presenting cells that would facilitate the development of both B and T cell-mediated autoimmunity. The repeated cytokine productions are achieved by the repeated infection of naive B-lymphocytes and proliferation of type III latency cells that produce inflammatory cytokines. Presentation of viral or self-antigens by EBV type III latency B lymphocytes may promote autoreactive B cell and T cell proliferation, which can be amplified by type III latency cells-mediated cytokines productions. Different autoimmune diseases may require different kinds of pathogenic immune cells and/or specific cytokines. Frequency of the replenishment of EBV type III latency cells may determine the specific effect of the promoter functions. A specific initiator plus EBV-mediated common promoter function may lead to development of a specific autoimmune disease and link EBV-infection to a variety of autoimmunity.

A new strategy to prepare high-performance copper azide film for micro-initiator.

Copper azide (CA) has gradually become the chosen priming agent for microexplosive devices as a lead-free green priming agent. However, charge loading is challenging due to its high electrostatic sensitivity, severely limiting its practical application. In this study, copper hydroxide particles were evenly coated on the surface of carbon fiber using electrospinning and quick hot-pressing, and CA-based composites with uniform load were created using thein situazide technique while keeping good film characteristics. The produced CA-HP film has an electroostatic sensitivity of 3.8 mJ, which is much higher than the raw material of 0.05 mJ. The flame sensitivity has also been increased from 45 to 51 cm, and the use safety has been considerably enhanced. Furthermore, hot-pressed CA-HP films can improve the film's qualities, such as easy cutting and processing into the required shape, compatibility with MEMS processes, and the ability to successfully detonate secondary explosives with only 1 mg. This novel coupling technology expands the possibilities for developing high-safety primers for micro-initiator.

Lamotrigine compromises the fidelity of initiator tRNA recruitment to the ribosomal P-site by IF2 and the RbfA release from 30S ribosomes in Escherichia coli.

Lamotrigine (Ltg), an anticonvulsant drug, targets initiation factor 2 (IF2), compromises ribosome biogenesis and causes toxicity to Escherichia coli. However, our understanding of Ltg toxicity in E. coli remains unclear. While our in vitro assays reveal no effects of Ltg on the ribosome-dependent GTPase activity of IF2 or its role in initiation as measured by dipeptide formation in a fast kinetics assay, the in vivo experiments show that Ltg causes accumulation of the 17S precursor of 16S rRNA and leads to a decrease in polysome levels in E. coli. IF2 overexpression in E. coli increases Ltg toxicity. However, the overexpression of initiator tRNA (i-tRNA) protects it from the Ltg toxicity. The depletion of i-tRNA or overexpression of its 3GC mutant (lacking the characteristic 3GC base pairs in anticodon stem) enhances Ltg toxicity, and this enhancement in toxicity is synthetic with IF2 overexpression. The Ltg treatment itself causes a detectable increase in IF2 levels in E. coli and allows initiation with an elongator tRNA, suggesting compromise in the fidelity/specificity of IF2 function. Also, Ltg causes increased accumulation of ribosome-binding factor A (RbfA) on 30S ribosomal subunit. Based on our genetic and biochemical investigations, we show that Ltg compromises the function of i-tRNA/IF2 complex in ribosome maturation.

Preparation of open tubular capillary column covalently coated with polystyrene sulfonate with 4,4'-Azobis(4-cyanopentanoyl chloride) as polymerization initiator for electrochromatographic separation of alkaloids, sulfonamides, and peptides.

An open tubular capillary electrochromatography column covalently bonded with polystyrene sulfonate was prepared via in situ polymerization using functionalized Azo-initiator 4,4'-Azobis(4-cyanopentanoyl chloride). Scanning electron, fluorescence, and atomic force microscopy techniques showed the formation of a relatively rough layer of polymer. In addition, -CN and C = O stretching vibrations from infrared spectroscopy proved the successful immobilization of the azo-initiator through covalent bonding and X-ray photoelectron spectroscopy confirmed the elemental composition of the formed polymer layer. The prepared column was found to be appropriate for small and medium-sized molecules separation. Compared to bare fused silica capillary column higher selectivity and resolution were obtained for the separation of alkaloids, sulfonamides, and peptides as a result of the electrostatic and pi-pi stacking interactions between the small organic molecules and the coated column without compromising the electroosmotic flow mobility. Separation efficiency was also increased compared to the bare capillary for the separation of alkaloids (about 1.5 times). Moreover, intraday, inter-day, intra-batch, and inter-batch relative standard deviation values of retention time and peak area of peptides were within 2% and 10%, respectively, indicating good repeatability of the column preparation procedure. The developed method for the covalent bonding of polymers through a functionalized azo-initiator could represent a promising stable method for the preparation of an open tubular column.

Comparative Study of Polymer-Grafted BaTiO3 Nanoparticles Synthesized Using Normal ATRP as Well as ATRP and ARGET-ATRP with Sacrificial Initiator with a Focus on Controlling the Polymer Graft Density and Molecular Weight.

Structurally well-defined polymer-grafted nanoparticle hybrids are highly sought after for a variety of applications, such as antifouling, mechanical reinforcement, separations, and sensing. Herein, we report the synthesis of poly(methyl methacrylate) grafted- and poly(styrene) grafted-BaTiO3 nanoparticles using activator regeneration via electron transfer (ARGET ATRP) with a sacrificial initiator, atom transfer radical polymerization (normal ATRP), and ATRP with sacrificial initiator, to understand the role of the polymerization procedure in influencing the structure of nanoparticle hybrids. Irrespective of the polymerization procedure adopted for the synthesis of nanoparticle hybrids, we noticed PS grafted on the nanoparticles showed moderation in molecular weight and graft density (ranging from 30,400 to 83,900 g/mol and 0.122 to 0.067 chain/nm2) compared to PMMA-grafted nanoparticles (ranging from 44,620 to 230,000 g/mol and 0.071 to 0.015 chain/nm2). Reducing the polymerization time during ATRP has a significant impact on the molecular weight of polymer brushes grafted on the nanoparticles. PMMA-grafted nanoparticles synthesized using ATRP had lower graft density and considerably higher molecular weight compared to PS-grafted nanoparticles. However, the addition of a sacrificial initiator during ATRP resulted in moderation of the molecular weight and graft density of PMMA-grafted nanoparticles. The use of a sacrificial initiator along with ARGET offered the best control in achieving lower molecular weight and narrow dispersity for both PS (37,870 g/mol and PDI of 1.259) and PMMA (44,620 g/mol and PDI of 1.263) nanoparticle hybrid systems.

Mechanochemical Synthesis of Stimuli Responsive Microgels.

Mechanochemical approaches are widely used for the efficient, solvent-free synthesis of organic molecules, however their applicability to the synthesis of functional polymers has remained underexplored. Herein, we demonstrate for the first time that mechanochemically triggered free-radical polymerization allows solvent- and initiator-free syntheses of structurally and morphologically well-defined complex functional macromolecular architectures, namely stimuliresponsive microgels. The developed mechanochemical polymerization approach is applicable to a variety of monomers and allows synthesizing microgels with tunable chemical structure, variable size, controlled number of crosslinks and reactive functional end-groups.

From Light to Structure: Photo Initiators for Radical Two-Photon Polymerization.

Two-photon polymerization (2PP) represents a powerful technique for the fabrication of precise three-dimensional structures on a micro- and nanometer scale for various applications. While many review articles are focusing on the used polymeric materials and their application in 2PP, in this review the class of two-photon photo initiators (2PI) used for radical polymerization is discussed in detail. Because the demand for highly efficient 2PI has increased in the last decades, different approaches in designing new efficient 2PIs occurred. This review summarizes the 2PIs known in literature and discusses their absorption behavior under one- and two-photon absorption (2PA) conditions, their two-photon cross sections (σTPA ) as well as their efficiency under 2PP conditions. Here, the photo initiators are grouped depending on their chromophore system (D-π-A-π-D, D-π-D, etc.). Their polymerization efficiencies are evaluated by fabrication windows (FW) depending on different laser intensities and writing speeds.

Immobilization of 3,5-dimethylphenyl carbamate of cellulose and amylose on silica by photochemical and thermal radical processes.

The immobilization of cellulose 3,5-dimethylphenyl carbamate and amylose 3,5-dimethylphenyl carbamate on silica gel carrier was achieved by using photochemical and thermal processes. Both approaches provide an easy access to materials which were applied as chiral stationary phases (CSPs) for the chromatographic resolution of racemic molecules. The influence of parameters such as irradiation time and solvent on immobilization effectiveness was investigated. For the thermal processes, azo-bis-isobutyrontrile and di-tert-butyl peroxide were evaluated as radical initiators. The influence of parameters such as amount of radical initiator, solvent, temperature, and further handling operations on the immobilization rate was examined. The chiral recognition ability and the overall performance of the prepared immobilized phases were evaluated by injection of a series of racemic compounds onto packed HPLC columns. As there is almost no limitation of organic solvent types that can be used as mobile phases with the immobilized CSPs, they can be applied under chromatographic conditions which are prohibited with the corresponding non-bonded CSPs. This extended applicability considerably broadens the options for improving enantioselectivity and resolving chiral compounds which are not or only poorly soluble in the conventional mobile phases.