Cap Structure Research Articles

Translation Initiation Regulated by RNA-Binding Protein in Mammals: The Modulation of Translation Initiation Complex by Trans-Acting Factors.

Protein synthesis is tightly regulated at each step of translation. In particular, the formation of the basic cap-binding complex, eukaryotic initiation factor 4F (eIF4F) complex, on the 5′ cap structure of mRNA is positioned as the rate-limiting step, and various cis-elements on mRNA contribute to fine-tune spatiotemporal protein expression. The cis-element on mRNAs is recognized and bound to the trans-acting factors, which enable the regulation of the translation rate or mRNA stability. In this review, we focus on the molecular mechanism of how the assembly of the eIF4F complex is regulated on the cap structure of mRNAs. We also summarize the fine-tuned regulation of translation initiation by various trans-acting factors through cis-elements on mRNAs.

Pile Foundation Design and Analysis of Teaching Building in A High School

The foundation design should adhere to the principles of adapting measures to local conditions, using local materials, protecting the environment and saving resources. Based on the geotechnical engineering survey data, the design should be carried out by comprehensively considering the factors such as structure type, material situation and construction conditions. The pile foundation design is adopted in this project. includes the determination of pile end bearing layer and pile length, the determination of vertical bearing capacity of single pile, the calculation of pile number and pile layout form, the checking calculation of pile foundation bearing capacity and settlement, the design and checking calculation of pile body structure, the design and checking calculation of pile cap. Until all requirements of the specification are met.

Anatomical Structure and Ecological of Cephalanthera damasonium (Mill.) Druce and Its on Contribution to the Taxonomy of Orchidaceae

In this study, in the present study reveals the morphological, anatomical and ecological characteristic of Cephalanthera damasonium (Mill.) Druce in Turkey. Plant materials of Cephalanthera species were collected from one population, between 2018 in Eskişehir/Turkey. Cephalanthera damasonium samples were analyzed for 7 anatomical and soil characters and habitat properties. It was investigated micrometrically in the anatomy of Cephalanthera damasonium (Mill.) Druce. In morphological investigations, the structure of flower, lateral sepal, petal, dorsal sepal, lip, anther cap and column was determined. The findings were compared with those in Flora of Turkey. to habitat definition, Cephalanthera damasonium grew up to 800 m to 1200 m.

Translation Initiation Factor eIF4E Positively Modulates Conidiogenesis, Appressorium Formation, Host Invasion and Stress Homeostasis in the Filamentous Fungi Magnaporthe oryzae.

Translation initiation factor eIF4E generally mediates the recognition of the 5’cap structure of mRNA during the recruitment of the ribosomes to capped mRNA. Although the eIF4E has been shown to regulate stress response in Schizosaccharomyces pombe positively, there is no direct experimental evidence for the contributions of eIF4E to both physiological and pathogenic development of filamentous fungi. We generated Magnaporthe oryzae eIF4E (MoeIF4E3) gene deletion strains using homologous recombination strategies. Phenotypic and biochemical analyses of MoeIF4E3 defective strains showed that the deletion of MoeIF4E3 triggered a significant reduction in growth and conidiogenesis. We also showed that disruption of MoeIF4E3 partially impaired conidia germination, appressorium integrity and attenuated the pathogenicity of ΔMoeif4e3 strains. In summary, this study provides experimental insights into the contributions of the eIF4E3 to the development of filamentous fungi. Additionally, these observations underscored the need for a comprehensive evaluation of the translational regulatory machinery in phytopathogenic fungi during pathogen-host interaction progression.

Structural insights into dpCoA-RNA decapping by NudC

ABSTRACT Various kinds of cap structures, such as m7G, triphosphate groups, NAD and dpCoA, protect the 5′ terminus of RNA. The cap structures bond covalently to RNA and affect its stability, translation, and transport. The removal of the caps is mainly executed by Nudix hydrolase family proteins, including Dcp2, RppH and NudC. Numerous efforts have been made to elucidate the mechanism underlying the removal of m7G, triphosphate group, and NAD caps. In contrast, few studies related to the cleavage of the RNA dpCoA cap have been conducted. Here, we report the hydrolytic activity of Escherichia coli NudC towards dpCoA and dpCoA-capped RNA in vitro. We also determined the crystal structure of dimeric NudC in complex with dpCoA at 2.0 Å resolution. Structural analysis revealed that dpCoA is recognized and hydrolyzed in a manner similar to NAD. In addition, NudC may also remove other dinucleotide derivative caps of RNA, which comprise the AMP moieties. NudC homologs in Saccharomyces cerevisiae and Arabidopsis thaliana exhibited similar dpCoA decapping (deCoAping) activity. These results together indicate a conserved mechanism underpinning the hydrolysis of dpCoA-capped RNA in both prokaryotes and eukaryotes.

Analysis of tower foundation of long span single tower cable stayed bridge

The pylon is an important stressed structure in the single pylon cable-stayed bridge. The rationality of bearing platform and pile foundation of pylon foundation is one of the key research contents in the design of single pylon cable-stayed bridge. The main bridge of Tarim bridge in Xinjiang is a single tower double span cable-stayed bridge with span arrangement of (41 + 168 + 168 + 41) m and total height of cable tower of 125m. Arc shaped concrete tower columns are adopted. The stress of cable tower foundation is complex. The stress analysis of foundation scheme is one of the key problems of this project. In this paper, the geological conditions, structural stress, economic rationality, construction convenience and other factors are comprehensively considered, the different foundation types are compared and analyzed, the reasonable foundation type and layout type are determined, and the stress of the pile and cap structure of the main tower foundation is calculated and analyzed. Through the solid finite element model, this paper analyzes the influence of the stiffness deformation of pile cap on the stress of pile group foundation. The calculation results show that the stress of dumbbell shaped pile cap is more reasonable than that of rectangular foundation pile cap, and the number of pile foundation and the calculated pile length are reduced in varying degrees. By adjusting the pile foundation arrangement under dumbbell shaped foundation, the stress of pile foundation can be more uniform, which can be used as the foundation for similar projects. The foundation design provides reference and reference.

Chemomechanical Simulation of Microtubule Dynamics With Explicit Lateral Bond Dynamics

We introduce and parameterize a chemomechanical model of microtubule dynamics on the dimer level, which is based on the allosteric tubulin model and includes attachment, detachment and hydrolysis of tubulin dimers as well as stretching of lateral bonds, bending at longitudinal junctions, and the possibility of lateral bond rupture and formation. The model is computationally efficient such that we reach sufficiently long simulation times to observe repeated catastrophe and rescue events at realistic tubulin concentrations and hydrolysis rates, which allows us to deduce catastrophe and rescue rates. The chemomechanical model also allows us to gain insight into microscopic features of the GTP-tubulin cap structure and microscopic structural features triggering microtubule catastrophes and rescues. Dilution simulations show qualitative agreement with experiments. We also explore the consequences of a possible feedback of mechanical forces onto the hydrolysis process and the GTP-tubulin cap structure.

The methyltransferase domain of the Respiratory Syncytial Virus L protein catalyzes cap N7 and 2'-O-methylation.

Respiratory syncytial virus (RSV) is a negative sense single-stranded RNA virus and one of the main causes of severe lower respiratory tract infections in infants and young children. RSV RNA replication/transcription and capping are ensured by the viral Large (L) protein. The L protein contains a polymerase domain associated with a polyribonucleotidyl transferase domain in its N-terminus, and a methyltransferase (MTase) domain followed by the C-terminal domain (CTD) enriched in basic amino acids at its C-terminus. The MTase-CTD of Mononegavirales forms a clamp to accommodate RNA that is subsequently methylated on the cap structure and depending on the virus, on internal positions. These enzymatic activities are essential for efficient viral mRNA translation into proteins, and to prevent the recognition of uncapped viral RNA by innate immunity sensors. In this work, we demonstrated that the MTase-CTD of RSV, as well as the full-length L protein in complex with phosphoprotein (P), catalyzes the N7- and 2’-O-methylation of the cap structure of a short RNA sequence that corresponds to the 5’ end of viral mRNA. Using different experimental systems, we showed that the RSV MTase-CTD methylates the cap structure with a preference for N7-methylation as first reaction. However, we did not observe cap-independent internal methylation, as recently evidenced for the Ebola virus MTase. We also found that at μM concentrations, sinefungin, a S-adenosylmethionine analogue, inhibits the MTase activity of the RSV L protein and of the MTase-CTD domain. Altogether, these results suggest that the RSV MTase domain specifically recognizes viral RNA decorated by a cap structure and catalyzes its methylation, which is required for translation and innate immune system subversion.

Single‐Molecule Dynamics of Eukaryotic Translation Initiation

Translation initiation is a critical control point for eukaryotic gene expression. The molecular mechanism of initiation requires a highly dynamic and exquisitely coordinated interplay of mRNA with the translation machinery. Recognition of the mRNA 5ʹ cap structure by initiation factor eIF4F is a key early initiation step, and plays important roles in translational control. We have developed single-molecule fluorescence approaches to directly observe eIF4F–mRNA interaction in real time, both on individual mRNAs and at transcriptome scale with single-molecule resolution. Our data reveal order-of-magnitude variability across mRNAs for interaction of the cap-binding eIF4F subunit, eIF4E, and provide insights into how the eIF4F subunits eIF4G and eIF4A dynamically modulate cap recognition. The data implicate features throughout the mRNA as controlling cap recognition at the 5ʹ end, including a relationship between coding-sequence length and the accessibility of the cap for recognition. We have also developed a single-molecule assay to directly observe the initiation steps that follow eIF4F–mRNA recognition, i.e. 43S ribosomal pre-initiation complex recruitment and pre-initiation complex scanning to locate the start codon. Taken together, our results evoke a multi-layered, mRNA-centric mechanism to kinetically control translation initiation and confer differential sensitivity to distinct regulatory mechanisms.

Overexpression-based detection of translatable circular RNAs is vulnerable to coexistent linear RNA byproducts

In RNA field, the demarcation between coding and non-coding has been negotiated by the recent discovery of occasionally translated circular RNAs (circRNAs). Although absent of 5’ cap structure, circRNAs can be translated cap-independently. Complementary intron-mediated overexpression is one of the most utilized methodologies for circRNA research but not without bearing echoing skepticism for its poorly defined mechanism and latent coexistent side products. In this study, leveraging such circRNA overexpression system, we have interrogated the protein-coding potential of 30 human circRNAs containing infinite open reading frames in HEK293T cells. Surprisingly, pervasive translation signals are detected by immunoblotting. However, intensive mutagenesis reveals that numerous translation signals are generated independently of circRNA synthesis. We have developed a dual tag strategy to isolate translation noise and directly demonstrate that the spurious translation signals originate from cryptically spliced linear transcripts. The concomitant linear RNA byproducts, presumably concatemers, can be translated to allow pseudo rolling circle translation signals, and can involve backsplicing junction (BSJ) to disqualify the BSJ-based evidence for circRNA translation. We also find non-AUG start codons may engage in the translation initiation of circRNAs. Taken together, our systematic evaluation sheds light on heterogeneous translational outputs from circRNA overexpression vector and comes with a caveat that ectopic overexpression technique necessitates extremely rigorous control setup in circRNA translation and functional investigation.

Nanoslot metasurface design and characterization for enhanced organic light-emitting diodes

We investigate bottom-emitting organic light-emitting diodes (B-OLEDs) integrated with metasurface (MS) to analyze the effect of the structural parameters on the output performance. The performance of the MS-integrated B-OLED (MIB-OLED) is evaluated by out-coupling efficiency (OCE) and reflection of the ambient light, while attention is paid mainly to dielectric capping and metal structure of MS that may influence excitation of surface plasmon (SP). The results suggest that layer thicknesses affect the performance by as much as 10% for the OCE and up to 32% for reflectance. The OCE is in general weakly affected by the structural parameters of MS. In contrast, the reflectance characteristics are found to be dominated by localized SP that is largely determined by the length and the width of a unit slot of MS. An optimization factor introduced to evaluate the performance based on out-coupling power to the radiation mode and reflectance of MIB-OLEDs confirms that integration with MS improves performance by 16% over conventional planar structure. In particular, MIB-OLED is found to enhance OCE by 51% with Lambertian-like pattern. Enhanced performance is experimentally confirmed. The findings provide insights on how to optimize the MS structure to produce MIB-OLEDs with enhanced out-coupled power and contrast ratio.

New Hopes in Vaccine Technology: mRNA Vaccines

The major disadvantages of traditional virus vaccines are time constraints in development and difficulties in large-scale production. Therefore, there is a need to develop stronger and more versatile vaccine platforms. mRNA vaccines constitute a promising alternative to traditional vaccine approaches due to their high potential, rapid development capacity, low cost production and safe administration potential. Stability and translation of mRNA are crucial for a successful RNA vaccine. It is critical to determine mRNA purity, stability, and protein yield during the translation process. Therefore, engineering the RNA sequence, such as modification of the 5' cap structure, extension of the poly (A) tail, editing nucleotide sequences in non-coding (UTR) and coding (ORF) regions, or incorporating modified nucleotides into the structure, makes synthetic mRNA more translatable. Two classes of non-replicating and self-amplifying mRNA are used as vaccines. While non-replicating mRNA only encodes protein antigens of interest, self-amplifying mRNA also encodes proteins required for RNA replication. The transfer and formulation of mRNA vaccines to cells is crucial for determining the kinetics of antigen expression, protein amount, and strength of immune response. In order to achieve this success, mRNA vaccines are given to cells in various formats such as lipid nanoparticles, polymers, peptides, and naked mRNA to develop the most effective transfer material. Recent technological advances have eliminated the low efficiency in in vivo transfer and translation and have made this vaccine platform widespread in preclinical and clinical trials against various infectious diseases and cancers. Over the past decade, major technological innovations have made mRNA a promising therapeutic tool in the fields of vaccine development and protein replacement therapy. Nowadays, antigens, neutralizing antibodies and proteins with immunostimulating activity have become coded by mRNA vaccines. Although many mRNA vaccines appear to be effective in preclinical and clinical studies, there are still some issues to be improved in terms of transfer efficiency, targeting to specific cell types, and the reliability of transfer devices. In this review, the latest developments and current challenges in the optimization, formulation and transfer of mRNA vaccines to cells with future development perspectives have been reviewed.

Shape optimization of quantum-dot caps for high color-rendering white light-emitting diodes studied by optical simulation

Conventional white lightings based on light-emitting diodes (LEDs) lack deep red, which is responsible for their low color rendering index (CRI). To apply red quantum-dot (QD) caps is one way to improve the color-rendering property of white LEDs. Red QD caps were fabricated using CdSe/ZnS QDs in the acrylic resin matrix and applied to conventional white LED lighting, which clearly showed a significant increase in the CRI, especially R9 associated with the strong red. Optical simulation was carried out to find out the optimized structure of the QD caps. The CRI increased while the optical efficiency decreased as the color conversion efficiency increased, which suggested that there should be a compromise between the two properties. It was found that to form a non-absorbing optical cavity in the QD cap was an effective way to achieve high CRI values while maintaining a moderately good optical efficiency.

The abundance and diversity of Basidiomycetes fungi in sago bark waste

This study was aimed to determine the abundance and diversity of Basidiomycetes fungi on sago bark waste. This research was conducted in January-February 2020 at Tondok Alla village, Telluwanua district, Palopo city (as location I) and Kalotok village, South Sabbang district, North Luwu regency (as location II). Climate data for the study period were obtained from the BMKG online website. The morphology of the fungi obtained from the sago bark waste was observed and identified morphologically for stalk color, cap structure and cap colour. The number of identified Basidiomycetes were analyzed to obtain relative abundance, species richness, evenness, Shannon Wiener diversity index, Simpson dominance index, and community similarity index. The climate observation results showed that, the average temperature was 27.74 (° C), 80.36% humidity, 12.37 mm of rainfall, and 4 hours / day of sun exposure. The fungi observation results showed that, several species of Basidiomycetes fungi was observed at both locations. Schizophyllum commune is the dominant species at both sites, and Ganoderma sp. the least. The species richness index, species evenness index, and diversity index at location I were higher than location II, while the Simpson dominance index was the highest in location II. Both locations have the same community structure based on the similarity index.

Effects of Interfacial Oxidization on Magnetic Damping and Spin-Orbit Torques.

We investigate the effects of interfacial oxidation on the perpendicular magnetic anisotropy, magnetic damping, and spin-orbit torques in heavy-metal (Pt)/ferromagnet (Co or NiFe)/capping (MgO/Ta, HfOx, or TaN) structures. At room temperature, the capping materials influence the effective surface magnetic anisotropy energy density, which is associated with the formation of interfacial magnetic oxides. The magnetic damping parameter of Co is considerably influenced by the capping material (especially MgO) while that of NiFe is not. This is possibly due to extra magnetic damping via spin-pumping process across the Co/CoO interface and incoherent magnon generation (spin fluctuation) developed in the antiferromagnetic CoO. It is also observed that both antidamping and field-like spin-orbit torque efficiencies vary with the capping material in the thickness ranges we examined. Our results reveal the crucial role of interfacial oxides on the perpendicular magnetic anisotropy, magnetic damping, and spin-orbit torques.

Incorporation mechanism of ZnO nanoparticles in PEO coating on 1060 Al alloy

Herein, a ZnO-doped plasma electrolytic oxidation (PEO) composite coating was prepared on the surface of a 1060 Al alloy by adding ZnO nanoparticles (ZnO-NPs) to the composite electrolytes of alkaline sodium silicate (Na 2 SiO 3 ) and sodium hexametaphosphate ((NaPO 3 ) 6 ). To efficiently investigate the coating's microstructure, the detached PEO coating was prepared without damage via an electrochemical method. The morphology and phase composition of the PEO coating were analyzed using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), transmission electron microscopy (TEM), and X-ray diffraction (XRD), and an incorporation model of ZnO-NPs was established. The results showed that the addition of ZnO-NPs slightly prolonged the anodic oxidation time and increased the breakdown voltage, whereas the working voltage and final voltage decreased slightly. The XRD results indicated that although the addition of ZnO-NPs did not result in the production of Zn-containing phases, it affected the formation and transformation reactions of other phases. SEM micrographs of the fractured cross-section of detached coating and coating/substrate interface indicated that the ZnO-NPs did not enter the interface layer, nor did it participate in the formation of the cap structure at the interface. Based on the experimental results and the “cascade discharge” model, an incorporation model of ZnO-NPs in PEO has been proposed. • A detached PEO coating with ZnO-NPs added was prepared by an electrochemical method. • The discharge channels were observed at the inside of the detached coating. • The formation mechanism of cap structure was discussed. • An incorporation model of ZnO-NPs in PEO coating was proposed.

Biological implications of decapping: beyond bulk mRNA decay.

It is well established that mRNA steady-state levels do not directly correlate with transcription rate. This is attributed to the multiple post-transcriptional mechanisms, which control both mRNA turnover and translation within eukaryotic cells. One such mechanism is the removal of the 5' end cap structure of RNAs (decapping). This 5' cap plays a fundamental role in cellular functions related to mRNA processing, transport, translation, quality control, and decay, while its chemical modifications influence the fate of cytoplasmic mRNAs. Decapping is a highly controlled process, performed by multiple decapping enzymes, and regulated by complex cellular networks. In this review, we provide an updated synopsis of 5' end modifications and functions, and give an overview of mRNA decapping enzymes, presenting their enzymatic properties. Focusing on DCP2 decapping enzyme, a major component on the 5'-3' mRNA decay pathway, we describe cis-elements and trans-acting factors that affect its activity, substrate specificity, and cellular localization. Finally, we discuss current knowledge on the biological functions of mRNA decapping and decay factors, highlighting the major questions that remain to be addressed.

Stem II-disrupting pseudoknot does not abolish ability of Senecavirus A IRES to initiate protein expression, but inhibits recovery of virus from cDNA clone

Senecavirus A (SVA) is classified into the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense, single-stranded and nonsegmented RNA, approximately 7300 nucleotides in length. A picornaviral genome is essentially an mRNA, which, albeit unmodified with 5′ cap structure, can still initiate protein expression by the internal ribosome entry site (IRES). The SVA genome contains a hepatitis C virus-like IRES, in which a pseudoknot structure plays an important role in initiating protein expression. In this study, we constructed a set of SVA (CH-LX-01-2016 strain) minigenomes with all combinations of point mutations in its pseudoknot stem II (PKS-II). The results showed that any combination of point mutations could not significantly interfere with the IRES to initiate protein expression. Further, we constructed a full-length SVA cDNA clone, in which the PKS-II-forming cDNA motif was subjected to site-directed mutagenesis for totally disrupting the PKS-II formation in IRES. Such a modified SVA cDNA clone was transfected into BSR-T7/5 cells, consequently demonstrating that the PKS-II-disrupting IRES interfered neither with protein expression nor with antigenome replication, whereas a competent SVA could not be rescued from the cDNA clone. It was speculated that the mutated motif possibly disrupted a packaging signal for virion assembly, therefore causing the failure of SVA rescue.

An immune epigenetic insight to COVID-19 infection.

Severe acute respiratory syndrome coronavirus-2 is a positive-sense RNA virus, a causal agent of ongoing COVID-19 pandemic. ACE2R methylation across three CpG sites (cg04013915, cg08559914, cg03536816) determines the host cell’s entry. It regulates ACE2 expression by controlling the SIRT1 and KDM5B activity. Further, it regulates Type I and III IFN response by modulating H3K27me3 and H3K4me3 histone mark. SARS-CoV-2 protein with bromodomain and protein E mimics bromodomain histones and evades from host immune response. The 2′-O MTases mimics the host’s cap1 structure and plays a vital role in immune evasion through Hsp90-mediated epigenetic process to hijack the infected cells. Although the current review highlighted the critical epigenetic events associated with SARS-CoV-2 immune evasion, the detailed mechanism is yet to be elucidated.

Molecular structure of stress granules and their role in the eukaryotic cell

Abstract Stress granules (SGs) are cytoplasmic structures found in eukaryotic cells, from yeast to human cells. They are made up of proteins, RNA and small ribosome subunits (40S). They arise as a result of the rapid shutdown of active protein biosynthesis in the cell, which is the result of the appearance of a stress factor. The mechanism of regulation of protein biosynthesis in response to stress takes place at two control nodes: (1) phosphorylation of the α subunit of the eIF2 factor as a result of the action of stress-recognizing kinases or by modulation of the mTOR pathway activity, which regulates the initiation of protein biosynthesis by the formation of a complex within the so-called cap structure. The protein arrest causes aggregation of the translation process components and other cell components (other proteins or mRNA molecules) into SGs. A lot of data indicates the active participation of SGs in metabolic processes, their control role over pro- and anti-apoptotic processes as well as in the development of cancer, neurodegenerative diseases and their defensive role in viral infections. Running title: Stress granules in the cell