Evolution of the Early Spliceosomal Complex—From Constitutive to Regulated Splicing

Pre-mRNA splicing is a major process in the regulated expression of genes in eukaryotes, and alternative splicing is used to generate different proteins from the same coding gene. Splicing is a catalytic process that removes introns and ligates exons to create the RNA sequence that codifies the final protein. While this is achieved in an autocatalytic process in ancestral group II introns in prokaryotes, the spliceosome has evolved during eukaryogenesis to assist in this process and to finally provide the opportunity for intron-specific splicing. In the early stage of splicing, the RNA 5′ and 3′ splice sites must be brought within proximity to correctly assemble the active spliceosome and perform the excision and ligation reactions. The assembly of this first complex, termed E-complex, is currently the least understood process. We focused in this review on the formation of the E-complex and compared its composition and function in three different organisms. We highlight the common ancestral mechanisms in S. cerevisiae, S. pombe, and mammals and conclude with a unifying model for intron definition in constitutive and regulated co-transcriptional splicing.

Investigation on the Preparation of Rice Straw-Derived Cellulose Acetate and Its Spinnability for Electrospinning

Rice straw-derived cellulose (RSC) with purity of 92 wt.% was successfully extracted from rice straw by a novel and facile strategy, which integrated the C2H5OH/H2O autocatalytic process, dilute alkali treatment and H2O2 bleaching process. Influencing factors of the cellulose extraction were systematically examined, such as ethanol concentration, alkali concentration, H2O2 bleaching process and so on; the optimal extraction conditions of cellulose was determined. A series of rice straw-derived cellulose acetate (RSCA) with different degree of substitution (DS) were prepared by the acetylation reaction; the effects of Ac2O/cellulose ratio, reaction temperature and reaction time on the acetylation reaction were investigated. Results of FTIR and XRD analysis demonstrated that highly purified RSC and RSCA were prepared comparing with the commercial cellulose and cellulose acetate. Solubility analysis of RSCA with different DS indicated as-prepared RSCA with DS of 2.82 possessed the best solubleness, which was suitable for electrospinning. Moreover, the flexible RSCA fibrous membrane was easily fabricated by a facile electrospinning method. Our proposed method provided a strategy for realizing the high-value utilization of waste rice straw resource, as prepared RSC and RSCA can be used as chemical raw material, and electrospun RSCA fibrous membrane has various applications in medical materials, food packaging, water purification and so on.

QM/MM Study of the Reactivity of Zeolite Bound Methoxy and Carbene Groups

<div>The conversion of methanol-to-hydrocarbons (MTH) is known to occur via an autocatalytic process in zeolites, where framework-bound methoxy species play a pivotal role, especially during catalyst induction. Recent NMR and FT-IR experimental studies suggest that methoxylated zeolites are able to produce hydrocarbons by a mechanism involving carbene migration and association. In order to understand these observations, we have performed QM/MM computational investigations on a range of reaction mechanisms for the reaction of zeolite bound methoxy and carbene groups, which are proposed to initiate hydrocarbon formation in the MTH process. Our simulations demonstrate that it is kinetically unfavourable for methyl species to form on the framework away from the zeolite acid site, and both kinetically and thermodynamically unfavourable for methyl groups to migrate through the framework and aggregate around an acid site. Formation of carbene moieties was considered as an alternative pathway to the formation of C-C bonds; however, the reaction energy for conversion of a methyl to a carbene is unfavourable. Metadynamics simulations help confirm further that methyl species at the framework acid sites would be more reactive towards formed C₂₊ species, rather than inter-framework migration and that the role of carbenes in the formation of the first –C bond will be via a concerted type of mechanism rather than stepwise. </div>

QM/MM Study of the Reactivity of Zeolite Bound Methoxy and Carbene Groups

<div>The conversion of methanol-to-hydrocarbons (MTH) is known to occur via an autocatalytic process in zeolites, where framework-bound methoxy species play a pivotal role, especially during catalyst induction. Recent NMR and FT-IR experimental studies suggest that methoxylated zeolites are able to produce hydrocarbons by a mechanism involving carbene migration and association. In order to understand these observations, we have performed QM/MM computational investigations on a range of reaction mechanisms for the reaction of zeolite bound methoxy and carbene groups, which are proposed to initiate hydrocarbon formation in the MTH process. Our simulations demonstrate that it is kinetically unfavourable for methyl species to form on the framework away from the zeolite acid site, and both kinetically and thermodynamically unfavourable for methyl groups to migrate through the framework and aggregate around an acid site. Formation of carbene moieties was considered as an alternative pathway to the formation of C-C bonds; however, the reaction energy for conversion of a methyl to a carbene is unfavourable. Metadynamics simulations help confirm further that methyl species at the framework acid sites would be more reactive towards formed C₂₊ species, rather than inter-framework migration and that the role of carbenes in the formation of the first –C bond will be via a concerted type of mechanism rather than stepwise. </div>

Intra-mitochondrial disulfide polymerization controls cancer cell necroptosis

In a biological system, energy-consuming reactions to attain a biological dissipative state are ubiquitous, and mimicking such reactions is a great challenge in synthetic chemistry. Herein, we report an intra-mitochondrial polymerization strategy for constructing macroscopic structures using a reactive oxygen species (ROS)-dissipative system. This is the first time that the occurrence of disulfide polymerization inside cancer mitochondria owing to the high ROS concentration of cancer mitochondria is reported. This polymerization hardly occurred inside cells owing to the intracellular reductive environment. The polymerization process of a thiol-containing monomer further increases the ROS level inside the mitochondria, thereby enabling the autocatalytic process to accelerate polymerization and induce mitochondrial dysfunction. This in-situ polymerization shows great potential for anticancer treatment against various cancer cell lines, including drug-resistant cancer cells.

Autocatalytic deoximation reactions driven by visible light

Photocatalytic deoximation reaction was found to be an autocatalytic process that occurs via free-radical mechanism. Understanding the mechanism may help chemical engineers to develop related techniques to avoid the decomposition of oximes.

QM/MM study of the reactivity of zeolite bound methoxy and carbene groups

The conversion of methanol-to-hydrocarbons (MTH) is known to occur via an autocatalytic process in zeolites, where framework-bound methoxy species play a pivotal role, especially during catalyst induction. Recent NMR and...

Enhancing Effect of Chloride Ions on the Autocatalytic Process of Ag(I) Reduction by Co(II) Complexes

In this work, the possibilities of increasing the rate of electroless silver plating without a rise in the concentration of reactants or elevation of temperature were studied. The effect of halide additive, namely chloride ions, on the rate of electroless silver deposition was investigated, using conventional chemical kinetics and electrochemical techniques. It was found that the deposition rate of electroless silver increased 2–3 times in the presence of 10–20 mM of chlorides, preserving sufficient stability of the solution.

Anomalous fluctuations and selective extinction in primordial replicators: a ‘struggle for life’ at the origin of biological homochirality

The prevalent presence of a single chiral variant of molecules in live organisms is one of the most distinctive signs of life as a global phenomenon. One of the greatest ambitions of biochemistry and astrobiology is to provide an explanation of this predominance. Several mechanisms were proposed in the past, from the propagation of chirality from a homo-chiral substrate to the amplification of effects associated with electro-weak interactions. Here, a different scenario is proposed: anomalous fluctuations associated with a self-replication scenario can lead to the selective extinction of primordial organisms using one of two enantiomers as an enzyme. These fluctuations arise spontaneously under very general conditions. The idea is based on three key points: (a) the simulation of early biological processes as a ‘board game’; (b) the presence of large fluctuations during an autocatalytic process; (c) the presence of a limited source of chemical energy, inducing a form of competition in a primordial replicator population. In order to demonstrate this mechanism, a computational model is developed, describing the ‘struggle for life’ of two different kinds of primordial replicators on a ‘chessboard’ with periodic boundary conditions; each replicator employs enzymes of different chirality on a non-chiral substrate, thereby with no selective advantage. The replication occurs randomly and with a fixed probability, providing that a sufficient amount of chemical energy is locally available. For the first time, our model includes the local balance of chemical energy in a molecular form on the substrate. The correlation between the chemical energy and the local populations is shown. Results clearly show that strong fluctuations in the number of individuals of each species and subsequent selective extinction events of one of the two species are observed. These studies may contribute to shed light on the most mysterious phase transition that occurred during the biochemical evolution of our planet.

Insights into the Maturation of Pernisine, a Subtilisin-Like Protease from the Hyperthermophilic Archaeon Aeropyrum pernix

ABSTRACT Pernisine is a subtilisin-like protease that was originally identified in the hyperthermophilic archaeon Aeropyrum pernix, which lives in extreme marine environments. Pernisine shows exceptional stability and activity due to the high-temperature conditions experienced by A. pernix. Pernisine is of interest for industrial purposes, as it is one of the few proteases that has demonstrated prion-degrading activity. Like other extracellular subtilisins, pernisine is synthesized in its inactive pro-form (pro-pernisine), which needs to undergo maturation to become proteolytically active. The maturation processes of mesophilic subtilisins have been investigated in detail; however, less is known about the maturation of their thermophilic homologs, such as pernisine. Here, we show that the structure of pro-pernisine is disordered in the absence of Ca2+ ions. In contrast to the mesophilic subtilisins, pro-pernisine requires Ca2+ ions to adopt the conformation suitable for its subsequent maturation. In addition to several Ca2+-binding sites that have been conserved from the thermostable Tk-subtilisin, pernisine has an additional insertion sequence with a Ca2+-binding motif. We demonstrate the importance of this insertion for efficient folding and stabilization of pernisine during its maturation. Moreover, analysis of the pernisine propeptide explains the high-temperature requirement for pro-pernisine maturation. Of note, the propeptide inhibits the pernisine catalytic domain more potently at high temperatures. After dissociation, the propeptide is destabilized at high temperatures only, which leads to its degradation and finally to pernisine activation. Our data provide new insights into and understanding of the thermostable subtilisin autoactivation mechanism. IMPORTANCE Enzymes from thermophilic organisms are of particular importance for use in industrial applications, due to their exceptional stability and activity. Pernisine, from the hyperthermophilic archaeon Aeropyrum pernix, is a proteolytic enzyme that can degrade infective prion proteins and thus has a potential use for disinfection of prion-contaminated surfaces. Like other subtilisin-like proteases, pernisine needs to mature through an autocatalytic process to become an active protease. In the present study, we address the maturation of pernisine and show that the process is regulated specifically at high temperatures by the propeptide. Furthermore, we demonstrate the importance of a unique Ca2+-binding insertion for stabilization of mature pernisine. Our results provide a novel understanding of thermostable subtilisin autoactivation, which might advance the development of these enzymes for commercial use.