Concerted Process Research Articles

Inactivation gating of Kv7.1 channels does not involve concerted cooperative subunit interactions

ABSTRACTInactivation is an intrinsic property of numerous voltage-gated K+ (Kv) channels and can occur by N-type or/and C-type mechanisms. N-type inactivation is a fast, voltage independent process, coupled to activation, with each inactivation particle of a tetrameric channel acting independently. In N-type inactivation, a single inactivation particle is necessary and sufficient to occlude the pore. C-type inactivation is a slower process, involving the outermost region of the pore and is mediated by a concerted, highly cooperative interaction between all four subunits. Inactivation of Kv7.1 channels does not exhibit the hallmarks of N- and C-type inactivation. Inactivation of WT Kv7.1 channels can be revealed by hooked tail currents that reflects the recovery from a fast and voltage-independent inactivation process. However, several Kv7.1 mutants such as the pore mutant L273F generate an additional voltage-dependent slow inactivation. The subunit interactions during this slow inactivation gating remain unexplored. The goal of the present study was to study the nature of subunit interactions along Kv7.1 inactivation gating, using concatenated tetrameric Kv7.1 channel and introducing sequentially into each of the four subunits the slow inactivating pore mutation L273F. Incorporating an incremental number of inactivating mutant subunits did not affect the inactivation kinetics but slowed down the recovery kinetics from inactivation. Results indicate that Kv7.1 inactivation gating is not compatible with a concerted cooperative process. Instead, adding an inactivating subunit L273F into the Kv7.1 tetramer incrementally stabilizes the inactivated state, which suggests that like for activation gating, Kv7.1 slow inactivation gating is not a concerted process.

Study on feature of ITS2 in 11 Perciformes species and the application on phylogenetic relationship

PDF HTML阅读 XML下载 导出引用 引用提醒 11种鲈形目鱼类ITS2特征及系统应用 DOI: 作者: 作者单位: 1. 中国科学院热带海洋生物资源与生态重点实验室, 广东 广州 510301;2. 中国科学院大学, 北京 100049;3. 中国科学院海洋研究所, 海洋生物分类与系统演化实验室, 山东 青岛 266071;4. 广东省应用海洋生物学重点实验室, 广东 广州 510301 作者简介: 武宝生(1991-),男,硕士,从事鱼类分类及系统进化研究.E-mail:wubaosheng15@mails.ucas.ac.cn 通讯作者: 中图分类号: S917;Q96 基金项目: 国家自然科学基金项目（31272273）. Study on feature of ITS2 in 11 Perciformes species and the application on phylogenetic relationship Author: Affiliation: 1. Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China;2. University of Chinese Academy of Sciences, Beijing 100049, China;3. Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;4. Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:ITS2（Internal transcribed spacer 2）是位于核糖体5.8S和28S基因之间的非编码序列。为了探讨该片段的多样性特征以及进化模式，本研究选取了鲈形目（Perciformes）5科11种鱼类为研究对象，共获得了444条ITS2克隆序列，其长度范围为332~515 bp。比较种内不同序列的长度发现，金带细鲹（）在种内存在32 bp的差异，这2种鱼类的差异较为明显；其余9种鱼类的长度相对比较保守，长度差异小于14 bp。依据11种鱼类的保守位点数、变异位点数、简约信息位点数、单倍型数、保守位点比例、单倍型多样性指数、核苷酸多样性等特征分析发现，种内存在着不同程度差异，特别是金带细鲹的ITS2序列存在着Type A、Type B和Type C 3种类型，各类型间差异较大。根据序列的多样性特征推断，金带细鲹和剑鱼的进化方式为非协同进化；蓝圆鲹（Alepes djedaba）和日本竹鱼䇲（Scomberoides tala）、布氏鲳鲹（Toxotes chatareus）和军曹鱼（）5种鱼类为协同进化；另外，协同和非协同进化状态与分类系统没有相关性。序列比对发现，大甲鲹种内存在着由协同进化方式演变为非严格的协同进化方式的过度序列；在金带细鲹的3个不同个体中，序列间存在着从协同进化、非严格的协同进化演变为非协同进化的3种进化方式。基于ITS2序列构建的11种鱼类的邻接系统树显示，每种鱼类的克隆都分别按种单独聚为一支，鲹科7属鱼类各属也是单独聚支，表明ITS2不仅可以用在种类的分子鉴定，同时也可以作为分子标记应用于鲹科和属级水平的系统关系研究。 Abstract:The nuclear ribosomal RNA (nrRNA) genes of eukaryotes are organized in clusters of tandem repeat units, including three genes (18S, 5.8S, and 28S) and two internal transcribed spacers (ITS1 and ITS2). The ITS2 is located between the 5.8S and 28S genes. Because multiple copies of ITS2 have different intra-and inter-species evolution rates, ITS2 is often used as the molecular marker to identify species or to infer the phylogenetic relationship at the rank of species or genera. In this study, 11 species from five families of Perciformes were selected as the representatives to investigate the characteristics and the evolutionary pattern of the ITS2 in fishes. A total of 444 cloning sequences of ITS2 were obtained from 24 samples through PCR and cloning methods. The length of these sequences ranged between 332-515 bp. A comparison of sequences within species found that the length of (32 bp) were extremely varied, and that of others, less than 14 bp, were relatively conservative. The evolutionary pattern of ITS2 of 11 species within species were conjectured based on the difference in several polymorphism characteristics, including the difference in length, conserved and variable sites, parsimony-informative site, the number of haploid type, proportion of conserved and variable sites, haploid type diversity index, nucleotide diversity and genetic diversity. The two out of 11 species () had obvious differences, especially the three different sequence types (Type A, Type B and Type C) detected in three individuals, suggesting a non-concerted evolution. Although, to a certain extent, length and variable sites were observed in four other species (, and S. leptolepis and , therefore, the four species were not subjected to strict concerted evolution (no-strict concerted evolution). The five other species (Toxotes chatareus, and ) almost had no intraspecific variations, suggesting a concerted evolution process. Meanwhile, there was no correlation between the evolution pattern of 11 species and the taxonomic system. In addition, sequence comparison revealed that transitive sequences between concerted evolution and non-concerted evolution were observed in , all three evolutionary patterns (concerted evolution, no-strict concerted evolution and non-concerted evolution) were detected in three individuals. Based on 444 cloning sequences of ITS2 from 11 species with as the outgroup, two phylogenetic trees were constructed using the neighborjoining and maximum likelihood methods. The results showed that both trees were largely congruent with each other. The topology showed that sequences from the same species clustered together and sequences from each genus of seven genera in Carangidae claded together. These results supported that the ITS2 is applicable as a molecular marker for species identification, but also useful for phylogenetic relation analysis at the rank of genus in Carangidae. 参考文献 相似文献 引证文献

Pastoralism and Land Tenure Transformation in Sub-Saharan Africa: Conflicting Policies and Priorities in Ngamiland, Botswana

In dryland Africa, access to land and water resources are central to pastoral livelihood activities. Policy intervention in these regions represents the outcome of concerted post-independence processes in which countries have committed to land tenure transformation as a policy objective. This was meant to create private, liberal property rights to replace communal customary tenure systems which were considered to be a constraint to development. Despite these efforts, decades of scientific research indicate that countries are still struggling to meet environmental sustainability objectives. Land degradation where it existed has not been halted and traditional pastoral livelihoods have been disrupted. The overall evidence base for policymaking remains weak as deficiencies in data or information on which management decisions were based led to poor policy performance. In a bid to strengthen understanding in this area, this study has a dual aim: 1. Using a systematic review of the literature, we examine the impact of land tenure transformation in pastoral areas in sub-Saharan Africa; 2. We analyse user-perspectives on land tenure transformation and pastoralists’ rights in Ngamiland, Botswana, so as to draw out the salient issues that must be addressed in order to reconcile pastoral tenure conflicts and land management in sub-Saharan Africa. Results from meta-analysis and case study show that land tenure transformation policies across pastoral areas are subject to similar challenges and consequences. Protecting pastoral land rights requires deliberate policy interventions that recognise pastoralism as a productive and efficient use of resources. Policymakers need to overcome anti-pastoral prejudice and focus on Sustainable Land Management goals. This entails establishing negotiated and flexible tenure frameworks that strengthen pastoralists’ participation in decision-making arenas by working with pastoral communities on the basis of understanding their livelihood system.

High-performance order processing in picking workstations

This paper investigates the order processing in picking workstations, which are among today’s most efficient order picking devices. A workstation is continuously supplied with storage bins containing stock keeping units (SKUs) from an interconnected storage system, so that a human worker only has to repack the items into customer bins. This way of unproductive work content, e.g., travel time, is eliminated and up to 1000 picks per hour is enabled. We aim at a concerted processing of picking orders and storage bins delivered from the storage system, such that an even more efficient picking process is enabled. We formalize the resulting order processing problem and present an efficient solution procedure. Our computational results show that the automated crane of the storage system feeding the picking workstation with bins can considerably be relieved by our procedure.

Synthesis of Diverse Nitrogen Heterocycles via Palladium‐Catalyzed Tandem Azide–Isocyanide Cross‐Coupling/Cyclization: Mechanistic Insight using Experimental and Theoretical Studies

AbstractA rapid and elegant tandem azide–isocyanide cross‐coupling/cyclization protocol has been developed based on a nitrene transfer reaction. The palladium‐catalyzed ligand‐free methodology led to the synthesis of three different heterocyclic scaffolds with excellent atom/step/redox economy. Studies based on first‐principles‐based quantum calculations and control experiments unraveled a concerted process of nitrene transfer reaction on isocyanides, ruling out the metallaaziridine intermediate reported earlier. This finding could pave the way for novel applications of nitrene transfer reactions to generate bioactive heterocycles.magnified image

Solvent effect on the electrochemical reduction of S-phenyl benzenethiosulfonate

The electrochemical reduction of S-phenyl benzenethiosulfonate (1) was investigated by cyclic voltammetry at different scan rates (0.1–60 V/s) using glassy carbon electrodes in three different solvents; acetonitrile, dimethyl sulfoxide, and dimethyl formamide. The initial electron transfer (ET) to the investigated compound follows a concerted process with the formation of a radical/ion pair before complete dissociation (“sticky” dissociative ET mechanism). Application of classical and “sticky” dissociative electron transfer theories, as well as theoretical calculations supported the proposed ET mechanism. The theoretical calculations showed that the LUMO of S-phenyl benzenethiosulfonate and SOMO of its reduced form are homed on the S-SO2 chemical bond with a low contribution on the rest of the molecule. This indicates that the incoming electron is directly injected to the chemical bond causing its cleavage. The controlled potential electrolysis of the investigated compound, monitored by high performance liquid chromatography and cyclic voltammetry, indicated the consumption of one electron per molecule, and final formation of diphenyl disulfide and phenyl sulfinate. All experimental and theoretical findings were used to propose the full reduction mechanism. Also, a solvent effect was observed on certain parameters including reduction peak potentials, transfer coefficient values, the strength of the interaction between the ion/radical fragments, and the chemical reaction processes following the first ET. This solvent effect was rationalized by comparison of the solvent’s properties.

Correlated Random Measures

ABSTRACTWe develop correlated random measures, random measures where the atom weights can exhibit a flexible pattern of dependence, and use them to develop powerful hierarchical Bayesian nonparametric models. Hierarchical Bayesian nonparametric models are usually built from completely random measures, a Poisson-process-based construction in which the atom weights are independent. Completely random measures imply strong independence assumptions in the corresponding hierarchical model, and these assumptions are often misplaced in real-world settings. Correlated random measures address this limitation. They model correlation within the measure by using a Gaussian process in concert with the Poisson process. With correlated random measures, for example, we can develop a latent feature model for which we can infer both the properties of the latent features and their dependency pattern. We develop several other examples as well. We study a correlated random measure model of pairwise count data. We derive an efficient variational inference algorithm and show improved predictive performance on large datasets of documents, web clicks, and electronic health records. Supplementary materials for this article are available online.

Exciton-Coupled Electron Transfer Process Controlled by Non-Markovian Environments.

We theoretically investigate an exciton-coupled electron transfer (XCET) process that is conversion of an exciton into a charge transfer state. This conversion happens in an exciton transfer (XT) process, and the electron moves away in an electron transfer (ET) process in multiple environments (baths). This XCET process plays an essential role in the harvesting of solar energy in biological and photovoltaic materials. We develop a practical theoretical model to study the efficiency of the XCET process that occurs either in consecutive or concerted processes under the influence of non-Markovian baths. The role of quantum coherence in the XT-ET system and the baths is investigated using reduced hierarchal equations of motion (HEOM). This model includes independent baths for each XT and ET state, in addition to a XCET bath for the conversion process. We found that, while quantum system-bath coherence is important in the XT and ET processes, coherence between the XT and ET processes must be suppressed in order to realize that an efficient irreversible XCET process through the weak off-diagonal interaction between the XT and ET bridge sites arises from an XCET bath.

Cyclic C-F-Metal Containig Species. Solid State and Computational Examples

This article examines the results of research published between 2000 and 2012, which found experimental evidence of cyclic species containing the fragment carbon-fluorine-transition metal. 25 Examples (numbered throughout this paper) with 20 different metals and a wide variety of chemical environments have been gathered. A similar analysis brings together almost 40 transitional states and intermediates resulting from theoretical work studying the transition metal mediated carbon-fluorine bond activation. Among other aspects, this review is useful to recognize the specific characteristics which determine whether the C-F activation process is carried out through a concerted process, a mechanism assisted by auxiliary ligands or by free radicals.

Ambidentate Ligand Reactivity with the Rhenium(I) Compounds [BrRe(CO)4]2 and cis‐BrRe(CO)4L: A Kinetic and Mechanistic Study

The reaction of the halo‐bridged dimer [BrRe(CO)4]2 with the ambidentate donor 2‐(diphenylphosphanyl)pyridine (PN) has been investigated. The substitution reaction is rapid at room temperature and regioselective for phosphorus coordination to yield exclusively cis‐BrRe(CO)4(κP‐PN) (1). Thermolysis of 1 furnishes the PN‐chelated product fac‐BrRe(CO)3(κP,N‐PN) (2) and CO. The kinetics for the conversion of 1 → 2 + CO have been measured by UV/Vis spectroscopy in toluene over the temperature range of 323–343 K. On the basis of the activation parameters [ΔH‡ = 28.0(0.9) kcal/mol and ΔS‡ = 31(3) eu], a dissociative process is supported, and this was corroborated by electronic structure calculations. The regioselectivity in the ligand‐substitution reaction involving [BrRe(CO)4]2 and the tridentate donor 6‐(diphenylphosphanyl)‐2‐formylpyridine (PON) was also studied, and consistent with the PN donor, only the κP‐product, cis‐BrRe(CO)4(κP‐PON) (3) is formed. The reaction of the dimer [BrRe(CO)4]2 with 2‐(diphenylphosphanyl)pyridine (PN) has been computationally modeled by DFT calculations. The energetics for the creation of an unsaturated intermediate through the cleavage of one of the bridging bromide ligands, followed by the addition of the donor to the unsaturated rhenium center versus the direct attack of the pnictogen donor on the dimer have been evaluated. The latter process is computed as the preferred route for dimer activation, with an attack of the pyridyl moiety slightly favored compared to the phosphine moiety. The computed pnictogen preference agrees with the kinetic data published by Zingales and coworkers. Concerning the reaction of the PN ligand with [BrRe(CO)4]2, we predict the initial formation of the κN‐isomer of 1 as the kinetic product of substitution, which in turn undergoes a rapid isomerization to furnish the thermodynamically more stable κP‐isomer through a reversible ligand dissociation process. The intramolecular linkage isomerization of κN‐1 to κP‐1 in 1 was also investigated by DFT, and the concerted process was found to lie 6.5 kcal/mol above the two‐step process involving ligand dissociation.

Mechanistic insights into the γ-elimination reaction of l-methionine catalyzed by methionine γ-lyase (MGL)

The γ-elimination mechanism of l-methionine catalyzed by methionine γ-lyase was studied by employing the combined quantum mechanics and molecular (QM/MM) calculations. Based on the two crystal structures of methionine γ-lyase from Clostridium sporogenes and Citrobacter freundii, a computational model that contains the enzyme and the external aldimine intermediate was constructed. According to the results of our calculations, the whole catalytic reaction can be divided into two parts. Part I describes the formation of external aldimine intermediate from the internal aldimine intermediate, in which the key protonation step within the tetrahedral intermediate (IM2) should require the assistance of one water molecule, and the dissociation of Lys210 from the internal aldimine intermediate corresponds to an overall energy barrier of 13.5 kcal/mol. In Part II, the external aldimine intermediate converts to the aminocrotonate intermediate, which contains complex asynchronous and concerted proton transfer processes, including those of Cα-proton and Cβ-proton of the substrate as well as the C4′-proton of PLP, in which the pocket residues Tyr113 and Lys210 play key roles. The abstraction of Cβ-proton and the transfer of C4′-proton correspond to very similar barrier heights (16.5 and 16.2 kcal/mol) on the potential energy surface, implying that both steps are possibly rate-limiting. Besides, the calculated overall energy barrier is close to the free energy barrier estimated from the experiment (16.3 kcal/mol). These results may provide useful information for further understanding the catalysis of pyridoxal 5′-phosphate (PLP)-dependent lyase.

CXCL1 and CXCL2 Regulate NLRP3 Inflammasome Activation via G-Protein–Coupled Receptor CXCR2

Inflammation is an extensively concerted process that confers protection to the host encountering immune insult. The major inflammatory mediators include IL-1 family members, such as IL-1β, and the functional activation of such molecules is arbitrated by their regulated cleavage brought about by components of a multiprotein complex called inflammasome. In this context, NLR family pyrin domain containing 3 (NLRP3) inflammasome activation often acts as a rate-limiting step in regulating critical cell-fate decisions in various inflammatory scenarios. In this study, we identify the G-protein-coupled receptor CXCR2 (recognizing chemokines CXCL1 and CXCL2) as another arm feeding into the regulated activation of NLRP3 inflammasome in macrophages. We demonstrate that in vivo blocking of CXCL1 and CXCL2 can significantly reduce the Mycobacterium tuberculosis-induced bioactive IL-1β production. Further, CXCL1 could amplify the inflammasome activation in in vivo mouse models of carrageenan-induced inflammation in footpads and air pouches. The mechanistic insights revealed CXCR2-driven protein kinase C μ-dependent integrin-linked kinase to be essential for CXCL1-mediated activation of NLRP3 inflammasome. Blocking the activity of integrin-linked kinase or protein kinase C μ either by small interfering RNA-mediated knockdown or pharmacological inhibitor compromised inflammasome activation and subsequent production of bioactive IL-1β. Taken together, our study demonstrates CXCR2-driven activation of NLRP3 inflammasome in macrophages and indicates a potential host-directed therapeutic target to limit the damaging inflammation associated with overt production of proinflammatory IL-1β.

Intermolecular Aryne Ene Reaction of Hantzsch Esters: Stable Covalent Ene Adducts from a 1,4-Dihydropyridine Reaction.

The reaction of arynes with 1,4-dihydropyridines affords 2-aryl-1,2-dihydropyridines or 2-methylene-3-aryl-1,2,3,4-tetrahydropyridines via a regioselective C-2 or C-3 arylation. These compounds are the first series of isolable and bench-stable covalent ene adducts formed between dihydropyridines and unsaturated substrates. Experimental studies and DFT calculations provide mechanistic support for a concerted intermolecular aryne ene process, which may have implications for NAD(P)H model reactions.

Nanoscale exponential distance dependence and electron-transfer model for intermolecular singlet exciton fission observed in rubrene-doped organic films

Abstract Singlet exciton fission, i.e., the splitting of a singlet exciton into two triplet excitons in molecular materials, is interesting due to its potential applications in organic photovoltaic devices. Traditionally, singlet fission can be explained by using an electron-transfer model in which twice concerted electron-transfer processes lead to the state conversion. In order to test this model, a highly efficient fission material, i.e., rubrene was mixed into other host materials which could be considered as spacers to separate doped rubrene molecules. Energy differences between LUMO levels of rubrene and host molecules constituted tunneling barriers for intermolecular electron-transfer between rubrene. Transient fluorescence spectroscopy was used to investigate the barrier effects in five series – two with varying barrier widths and three with varying barrier heights. The experimental results demonstrated that the transition rate of singlet fission exponentially decreased with the increasing distance between rubrene and the dynamics of fission process was apparently barrier-dependent. These findings could be regarded as clear confirmations of electron-transfer model for intermolecular singlet fission, and are of great importance for clarifying the true mechanism of singlet fission process.

Hydrophobic Patch of Ubiquitin is Important for its Optimal Activation by Ubiquitin Activating Enzyme E1.

Protein ubiquitination plays a role in essentially every process in eukaryotic cells. The attachment of ubiquitin (Ub) or Ub-like (UBL) proteins to target proteins is achieved by parallel but distinct cascades of enzymatic reactions involving three enzymes: E1, E2, and E3. The E1 enzyme functions at the apex of this pathway and plays a critical role in activating the C-terminus of ubiquitin or UBL, which is an essential step that triggers subsequent downstream transfer to their cognate E2s resulting in the fidelity of the Ub/UBL conjugation machinery. Despite the central role of the E1 enzyme in protein modification, a quantitative method to measure Ub/UBL activation by E1 is lacking. Here, we present a mass spectrometry-based assay to accurately measure the activation of Ub/UBL by E1 independent of the E2/E3 enzymes. Our method does not require radiolabeling of any components and therefore can be used in any biochemical laboratory having access to a mass spectrometer. This method allowed us to dissect the concerted process of E1-E2-catalyzed Ub conjugation in order to separately characterize the process of Ub activation and how it is affected by select mutations and other factors. We found that the hydrophobic patch of Ub is important for the optimal activation of Ub by E1. We further show that the blockers of the Ub-proteasome system such as ubistatin and fullerenol inhibit Ub activation by E1. Interestingly, our data indicate that the phosphorylation of Ub at the S65 position augments its activation by the E1 enzyme.

Three-body dissociation of OCS3+ : separating sequential and concerted pathways

SynopsisThree body fragmentation pathways of OCS3+ molecular ion leading to detection of C+ + O+ + S+ in coincidence have been studied using the technique of recoil ion momentum spectroscopy. This fragmentation can occur either via a one step concerted process or a two step sequential process. In the first step of the sequential pathway either CO2+ or CS2+ is formed. By separating the events coming from the two processes, branching ratios are determined and the possible electronic states associated with the intermediate CO2+ or CS2+ have been identified.

The [3+2] cycloaddition reaction in CpRu(allyl)(acetylene)

The transition metal-mediated coupling of allyl and alkyne ligands to yield cyclopentadienyl and pentadienyl compounds has been studied theoretically using M06 DFT calculations using CpRu(allyl)(acetylene) as a representative example. We find that the first step in the mechanism is the formation of a 16-electron α, π-vinyl olefin intermediate, whereas the alternative, least-motion 3+2 cycloaddition via a concerted process was calculated to lie at a prohibitively high energy and has the characteristics of a symmetry forbidden reaction. The 3+2 concerted path is shown to be unlikely for η3-allyl complexes in general. There are two competing mechanisms, which lead to Cp2Ru + H2 or CpRu(η5-pentadienyl). The pentadienyl product is predicted to form by either the rearrangement of the α, π-vinyl olefin complex or an electrocyclic ring opening of a cyclopentadiene intermediate. The alternative mechanism involves a ring closure of the α, π-vinyl olefin intermediate to yield CpRu(H)(cyclopentadiene). Four mechanistic scenarios were investigated for the reductive elimination of H2 to give Cp2Ru. The lowest energy process occurs via CpRu(H)2(η3-Cp). The other three possibilities are symmetry forbidden. It is shown that the partitioning of pentadienyl versus cyclopentadienyl products depends on the electronic characteristics of the metal. As the transition metal becomes more electron rich, the pathway to the pentadienyl product becomes more favored. Calculations on CpCo(π-allyl)(acetylene)+ and CpTc(π-allyl)(acetylene)− are in agreement with this hypothesis.

Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation.

In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding.

MicroRNA-driven deregulation of cytokine expression helps development of drug resistance in metastatic melanoma

microRNAs are major components of the eukaryotic post-transcriptional machinery and are frequently deregulated during cancer development. Increasing evidence points to them also as key players in the establishment of drug resistance. In this review, we provide an updated overview of the role of miRNAs in melanoma development and drug resistance and postulate that they are able to drive these processes in concert with deregulation of inflammatory and angiogenic cytokine expression. Notably, we have identified by querying the Cancer Genome Atlas database, a defined set of miRNAs which mostly have an impact on the development of melanoma and have recognized the main downstream pathways controlled by them. Most importantly, these miRNAs, which are down-regulated in metastatic melanomas as compared to primary tumors, are also able to predict prognosis of BRAF-mutated melanoma patients. Finally, we discuss the possibility that a common miRNA signature characterizes not only acquired resistance to MAPKi but also innate resistance to anti-PD-1 immunotherapy, since these conditions are both associated with alterations of the same pro-angiogenetic and pro-inflammatory pathways.

Boosting LPMO-driven lignocellulose degradation by polyphenol oxidase-activated lignin building blocks

BackgroundMany fungi boost the deconstruction of lignocellulosic plant biomass via oxidation using lytic polysaccharide monooxygenases (LPMOs). The application of LPMOs is expected to contribute to ecologically friendly conversion of biomass into fuels and chemicals. Moreover, applications of LPMO-modified cellulose-based products may be envisaged within the food or material industry.ResultsHere, we show an up to 75-fold improvement in LPMO-driven cellulose degradation using polyphenol oxidase-activated lignin building blocks. This concerted enzymatic process involves the initial conversion of monophenols into diphenols by the polyphenol oxidase MtPPO7 from Myceliophthora thermophila C1 and the subsequent oxidation of cellulose by MtLPMO9B. Interestingly, MtPPO7 shows preference towards lignin-derived methoxylated monophenols. Sequence analysis of genomes of 336 Ascomycota and 208 Basidiomycota reveals a high correlation between MtPPO7 and AA9 LPMO genes.ConclusionsThe activity towards methoxylated phenolic compounds distinguishes MtPPO7 from well-known PPOs, such as tyrosinases, and ensures that MtPPO7 is an excellent redox partner of LPMOs. The correlation between MtPPO7 and AA9 LPMO genes is indicative for the importance of the coupled action of different monooxygenases in the concerted degradation of lignocellulosic biomass. These results will contribute to a better understanding in both lignin deconstruction and enzymatic lignocellulose oxidation and potentially improve the exploration of eco-friendly routes for biomass utilization in a circular economy.