Crystal Structure of the S. solfataricus Archaeal Exosome Reveals Conformational Flexibility in the RNA-Binding Ring

The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry.Here we report an asymmetric 2.9 A Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation.This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing

Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from the In-Silico World

The SARS CoV-2 pandemic has affected millions of people around the globe. Despite many efforts to find some effective medicines against SARS CoV-2, no established therapeutics are available yet. The use of phytochemicals as antiviral agents provides hope against the proliferation of SARS-CoV-2. Several natural compounds were analyzed by virtual screening against six SARS CoV-2 protein targets using molecular docking simulations in the present study. More than a hundred plant-derived secondary metabolites have been docked, including alkaloids, flavonoids, coumarins, and steroids. SARS CoV-2 protein targets include Main protease (M(Pro)), Papain-like protease (PL(pro)), RNA-dependent RNA polymerase (RdRp), Spike glycoprotein (S), Helicase (Nsp13), and E-Channel protein. Phytochemicals were evaluated by molecular docking, and MD simulations were performed using the YASARA structure using a modified genetic algorithm and AMBER03 force field. Binding energies and dissociation constants allowed the identification of potentially active compounds. Ligand-protein interactions provide an insight into the mechanism and potential of identified compounds. Glycyrrhizin and its metabolite 18-β-glycyrrhetinic acid have shown a strong binding affinity for M(Pro), helicase, RdRp, spike, and E-channel proteins, while a flavonoid Baicalin also strongly binds against PL(pro) and RdRp. The use of identified phytochemicals may help to speed up the drug development and provide natural protection against SARS-CoV-2

Identification of floR Variants Associated With a Novel Tn4371-Like Integrative and Conjugative Element in Clinical Pseudomonas aeruginosa Isolates

Florfenicol is widely used to control respiratory diseases and intestinal infections in food animals. However, there are increasing reports about florfenicol resistance of various clinical pathogens. floR is a key resistance gene that mediates resistance to florfenicol and could spread among different bacteria. Here, we investigated the prevalence of floR in 430 Pseudomonas aeruginosa isolates from human clinical samples and identified three types of floR genes (designated floR, floR-T1 and floR-T2) in these isolates, with floR-T1 the most prevalent (5.3%, 23/430). FloR-T2 was a novel floR variant identified in this study, and exhibited less identity with other FloR proteins than FloRv. Moreover, floR-T1 and floR-T2 identified in P. aeruginosa strain TL1285 were functionally active and located on multi-drug resistance region of a novel incomplete Tn4371-like integrative and conjugative elements (ICE) in the chromosome. The expression of the two floR variants could be induced by florfenicol or chloramphenicol. These results indicated that the two floR variants played an essential role in the host’s resistance to amphenicol and the spreading of these floR variants might be related with the Tn4371 family ICE

Large-Scale in Vitro Transcription, RNA Purification and Chemical Probing Analysis

Background/Aims: RNA elements such as catalytic RNA, riboswitch, microRNA, and long non coding RNA (lncRNA) play central roles in many cellular processes. Studying diverse RNA functions require large quantities of RNA for precise structure analysis. Current RNA structure and function studies can benefit from improved RNA quantity and quality, simpler separation procedure and enhanced accuracy of structural analysis. Methods: Here we present an optimized protocol for analyzing the structure of any RNA, including in vitro transcription, size-exclusion chromatography (SEC) based denaturing purification and improved secondary structure analysis by chemical probing. Results: We observed that higher Mg2+, nucleoside triphosphate (NTP) concentrations and longer reaction duration can improve the RNA yield from in vitro transcription, specifically for longer and more complicated constructs. Our improved SEC-based denaturing RNA purification effectively halved the experiment duration and labor without introducing any contaminant. Finally, this study increased the accuracy and signal-to-noise ratio (SNR) of selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing for analyzing RNA structure. Conclusion: Part or all of our modified method can improve almost any RNA-related study from protein-RNA interaction analysis to crystallography

Ligand Recognition And Conformational Dynamics Of Sam-Binding Riboswitches

Riboswitches are recently discovered regulatory RNAs that directly relay environmental cues to the genetic regulat ory machinery. S box (SAM-I) and the SMK box (SAM-III) RNA are both S- Adenosyl -L-methionine (SAM) responsive riboswitches that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition respectively. The S box RNA is the most wide spread transcriptional riboswitch in Gram -positive bacteria, while the SMK RNA is a translational riboswitch in members of the Lactobacillales. Both RNAs bind specifically to SAM and feedback regulate the SAM biosynthetic pathway. However, these riboswitches share no sequence, structural or mechanistic homology. Our lab employs both X-ray crystallography and chemical probing to analyze their ligand recognition and mechanisms of gene repression. Our X-ray structures show that both the SMK and S box riboswitches fold into compact structures once bound to SAM, and that both RNAs adopt unique yet elegantly simple ways to specifically recognize SAM in favor of its close homolog, SAdenosyl-homocysteine (SAH). Further mutagenesis and chemical probing results show that both the SMK and S box RNA adopt extremely dynamic conformations in the absence of SAM, and certain structural elements outside the SAM-binding domain have profound effects on the conformation dynamics. The thermal melting experiments also showed that both riboswitches undergo unique unfolding processes when subject to increasing temperature s. Our findings suggest that these SA

Fabrication of Micro-Parts with High-Aspect Ratio Micro-Hole Array by Micro-Powder Injection Molding

The present study investigated high-aspect ratio micro-hole array parts which were made by ZrO2 micro-powder with different particle sizes and micro-powder injection molding technology. It analysed the influence of particle sizes on feedstock, debinding and sintering of ceramic nozzles with multi-micro-holes. The forming quality of ceramic nozzles with multi-micro-holes was discussed in this paper. The results show that the two mixed ZrO2 feedstocks have fine uniformity. The average deviation of the feedstock made with 200 nm powder was −2%, and the average deviation of the feedstock made with 100 nm powder was −7.1%. The sample showed certain sintering characteristics which provided better strength (11.10 MPa) to parts after debinding. The linear shrinkage and the density of the two powder samples at different sintering temperatures increased as the sintering temperature increased. If the temperature continued to increase, the linear shrinkage and the density decreased. The highest hardness and flexural strength values of the ZrO2 sample with 200 nm powder used were: 1265.5 HV and 453.4 MPa, and the crystalline particle size was 0.36 μm. The highest hardness and flexural strength values of the ZrO2 sample with 100 nm powder used were: 1425.8 HV and 503.6 MPa, and the crystalline particle size was 0.18 μm. The ceramic nozzles with multi-micro holes shrunk to nearly the same axial, radial and circumferential directions during sintering. After sintering, the roundness of ceramic micro-hole met the user requirements, and the circular hole had a high parallelism in the axial direction. The micropore diameter was 450 ± 5 μm, and it was possible to control the dimensional accuracy within 1.5% after sintering. The study presented a superior application prospect for high-aspect ratio micro hole array parts in aerospace, electronics and biomedicine

Fate of Fe3O4@NH2 in soil and their fixation effect to reduce lead translocation in two rice cultivars

Abstract The fate of nanoparticles in the ecological chain of agriculture has been concerned as their potential pollution and biological effect to humans with rapid development and massive emission of nanomaterials. Here, we found that two rice cultivars (Oryza sativa L) have different heavy metal accumulation results in the roots and shoots after 15 days growth. Two rice cultivars (Oryza sativa L), grown in soil containing magnetite (Fe3O4@NH2) nanoparticles and heavy metal simultaneous, showed less Pb uptake in the roots and shoots, compared with that without Fe3O4@NH2 added. The shape and magnetic properties of Fe3O4@NH2 have no obvious change; however, the transmission electron microscope (TEM) results showed the shell of Fe3O4@NH2 could be broken in the process of interaction with soil. These results suggested that magnetite nanoparticles, such as Fe3O4@NH2, could potentially be used as the recyclable heavy metal fixation materials for alleviating heavy metal poisoning to plant