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RNA degradation is critical for control of gene expression, and endonucleolytic cleavage– dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the cytoplasm and identified using the CAGE method. Although uncapped cleavage sites are widespread in eukaryotes, comparatively little information has been obtained about these sites using CAGE-based degradome analysis. Previously, we developed the truncated RNA-end sequencing (TREseq) method in plant species and used it to acquire comprehensive information about uncapped cleavage sites; we observed G-rich sequences near cleavage sites. However, it remains unclear whether this finding is general to other eukaryotes. In this study, we conducted TREseq analyses in fruit flies (Drosophila melanogaster) and budding yeast (Saccharomyces cerevisiae). The results revealed specific sequence features related to RNA cleavage in D. melanogaster and S. cerevisiae that were similar to sequence patterns in Arabidopsis thaliana. Although previous studies suggest that ribosome movements are important for determining cleavage position, feature selection using a random forest classifier showed that sequences around cleavage sites were major determinant for cleaved or uncleaved sites. Together, our results suggest that sequence features around cleavage sites are critical for determining cleavage position, and that sequence-specific endonucleolytic cleavage–dependent RNA degradation is highly conserved across eukaryotes.

Early cellular patterning is a critical step of embryonic development that determines the proper progression of morphogenesis in all metazoans. It relies on a series of rapid reductive divisions occurring simultaneously with the specification of the fate of different subsets of cells. Multiple species developmental strategies emerged in the form of a unique cleavage pattern with stereotyped division geometries. Cleavage geometries have long been associated to the emergence of canonical developmental features such as cell cycle asynchrony, zygotic genome activation and fate specification. Yet, the direct causal role of division positioning on blastomere cell behavior remain partially understood. Oriented and/or asymmetric divisions define blastomere cell sizes, contacts and positions, with potential immediate impact on cellular decisions, lineage specification and morphogenesis. Division positions also instruct daughter cells polarity, mechanics and geometries, thereby influencing subsequent division events, in an emergent interplay that may pattern early embryos independently of firm deterministic genetic programs. We here review the recent literature which helped to delineate mechanisms and functions of division positioning in early embryos.

The coronavirus 3C-like (3CL) protease is a Cysteine protease. It plays an important role in viral infection and immune escape by not only cleaving the viral polyprotein ORF1ab at 11 sites, but also cleaving the host proteins. However, there is still a lack of effective tools for determining the cleavage sites of the 3CL protease. This study systematically investigated the diversity of the cleavage sites of the coronavirus 3CL protease on the viral polyprotein, and found that the cleavage motif were highly conserved for viruses in the genera of Alphacoronavirus, Betacoronavirus and Gammacoronavirus. Strong residue preferences were observed at the neighboring positions of the cleavage sites. A random forest (RF) model was built to predict the cleavage sites of the coronavirus 3CL protease based on the representation of residues at cleavage site and neighboring positions by amino acid indexes, and the model achieved an AUC of 0.96 in cross-validations. The RF model was further tested on an independent test dataset composed of cleavage sites on host proteins, and achieved an AUC of 0.88 and a prediction precision of 0.80 when considering the accessibility of the cleavage site. Then, 1,079 human proteins were predicted to be cleaved by the 3CL protease by the RF model. These proteins were enriched in pathways related to neurodegenerative diseases and pathogen infection. Finally, a user-friendly online server named 3CLP was built to predict the cleavage sites of the coronavirus 3CL protease based on the RF model. Overall, the study not only provides an effective tool for identifying the cleavage sites of the 3CL protease, but also provides insights into the molecular mechanism underlying the pathogenicity of coronaviruses.

Resistance to chemotherapy is a leading cause of treatment failure. Drug-resistance mechanisms involve mutations in specific proteins or changes in their expression levels. It is commonly understood that resistance mutations happen randomly prior to treatment and are selected during the treatment. However, selection of drug-resistant mutants in culture could be achieved by multiple drug exposures of cloned genetically identical cells, and thus cannot result from selection of pre-existent mutations. Accordingly, adaptation must involve generation of mutations de-novo upon drug treatment. Here we explored the origin of resistance mutations to a widely used Top1 inhibitor irinotecan, which triggers DNA breaks, causing cytotoxicity. Resistance mechanism involved gradual accumulation of recurrent mutations in non-coding regions of DNA at Top1-cleavage sites. Surprisingly, cancer cells had higher number of such sites than reference genome, which may define their increased sensitivity to irinotecan. Homologous recombination repair of DNA double strand breaks at these sites following initial drug exposures gradually reverted cleavage-sensitive “cancer” sequences back to cleavage-resistant “normal” sequences. These mutations reduced generation of DNA breaks upon subsequent exposures, thus gradually increasing the drug resistance. Together, large target size for mutations and their Top1-guided generation lead to their gradual and rapid accumulation, synergistically accelerating development of resistance.Abstract Figure

DNA-based logic gates promote the development of molecular computing and show enormous potential in the fields of nanotechnology and biotechnology. Dumbbell oligonucleotides (DNA) with poly-thymine (poly-T) loops and a nicked random double strand have been demonstrated to be an efficient template for the formation of fluorescent copper nanoclusters (CuNCs) in our previous work. Herein, a new platform technology is presented with which to construct molecular logic gates by employing CuNCs probe as a basic output generator, coupling of functional nucleases as the inputs. Two dumbbell DNAs are used with the difference in stem length (8 bp and 16 bp, respectively). The degradation of DNA templates can be tuned by various nucleic acid enzymes, single-stranded nuclease (S1), double-stranded specific nuclease (DSN), E. coli DNA ligase, exonucleases I and III. Briefly, S1 can digest both DNA templates, while the cleavage ability of DSN will be resistant by the short stem of SS-DNA (short-stem DNA). Exonuclease I and III can degrade these two nicked DNA templates, which are inhibited due to the ligation of E. coli DNA ligase. With this novel strategy, a set of logic gates is successfully constructed at the molecular level, including “YES”, “PASS 0”, “OR”, “INHIBIT”, which take the advantages of no label, easy operation, fast speed, high efficiency and low cost. Furthermore, S1 nuclease, as the biomarker of numerous carcinogens, is selectively detected in the range of 0.05-50 U/mL with the detection limit of 0.005 U/mL (1 × 10−6 U) based on this platform.

Lignin is the most recalcitrant of the three components of lignocellulosic biomass. The strength and stability of the linkages have long been a great challenge for the degradation and valorization of lignin biomass to obtain bio-fuels and commercial chemicals. Up to now, the selective cleavage of C–O linkages of lignin to afford chemicals contains only C, H and O atoms. Our group has developed a cleavage/cross-coupling strategy for converting 4-O-5 linkage lignin model compounds into high value-added compounds. Herein, we present a palladium-catalyzed cleavage/cross-coupling of the β-O-4 lignin model compounds with amines via dual C–O bond cleavage for the preparation of benzyl amine compounds and phenols.

During metazoan early embryogenesis, the intracellular properties of proteins and organelles change dynamically through rapid cleavage. In particular, a change in the nucleus size is known to contribute to embryonic development-dependent cell cycle and gene expression regulation. Here, we compared the nuclear sizes of various blastomeres from developing Xenopus embryos and analyzed the mechanisms that control the nuclear expansion dynamics by manipulating the amount of intracellular components in a cell-free system. There was slower nuclear expansion during longer interphase durations in blastomeres from vegetal hemispheres than those from animal hemispheres. Furthermore, upon recapitulating interphase events by manipulating the concentration of yolk platelets, which are originally rich in the vegetal blastomeres, in cell-free cytoplasmic extracts, there was slower nuclear expansion and DNA replication as compared to normal yolk-free conditions. Under these conditions, the supplemented yolk platelets accumulated around the nucleus in a microtubule-dependent manner and impeded organization of the endoplasmic reticulum network. Overall, we propose that yolk platelets around the nucleus reduce membrane supply from the endoplasmic reticulum to the nucleus, resulting in slower nuclear expansion in the yolk-rich vegetal blastomeres.

3’-end processing of most human mRNAs is carried out by the cleavage and polyadenylation specificity factor (CPSF; CPF in yeast). Endonucleolytic cleavage of the nascent pre-mRNA defines the 3’-end of the mature transcript, which is important for mRNA localization, translation and stability. Cleavage must therefore be tightly regulated. Here, we reconstitute specific and efficient 3’-endonuclease activity of human CPSF with purified proteins. This requires the sevensubunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm) and, importantly, the multi-domain protein RBBP6. Unlike its yeast homologue Mpe1, which is a stable subunit of CPF, RBBP6 does not copurify with CPSF and is recruited in an RNA-dependent manner. Sequence and mutational analyses suggest that RBBP6 interacts with the WDR33 and CPSF73 subunits of CPSF. Thus, it is likely that the role of RBBP6 is conserved from yeast to human. Overall, our data are consistent with CPSF endonuclease activation and site-specific pre-mRNA cleavage being highly controlled to maintain fidelity in RNA processing.

Gasdermin proteins form large membrane pores in human cells that release immune cytokines and induce lytic cell death. Gasdermin pore formation is triggered by caspase-mediated cleavage during inflammasome signaling and is critical for defense against pathogens and cancer. Here we discover gasdermin homologs encoded in bacteria that execute prokaryotic cell death. Structures of bacterial gasdermins reveal a conserved pore-forming domain that is stabilized in the inactive state with a buried lipid modification. We demonstrate that bacterial gasdermins are activated by dedicated caspase-like proteases that catalyze site-specific cleavage and removal of an inhibitory C-terminal peptide. Release of autoinhibition induces the assembly of >200 Å pores that form a mesh-like structure and disrupt membrane integrity. These results demonstrate that caspase-mediated activation of gasdermins is an ancient form of regulated cell death shared between bacteria and animals.

The ubiquitously-expressed proteolytic enzyme furin is closely related to the pathogenesis of SARS-CoV-2 and therefore represents a key target for antiviral therapy. Based on bioinformatic analysis and pseudovirus tests, we discovered a second functional furin site located in the spike protein. Furin still increased the infectivity of mutated SARS-CoV-2 pseudovirus in 293T-ACE2 cells when the canonical polybasic cleavage site (682–686) was deleted. However, K814A mutation eliminated the enhancing effect of furin on virus infection. Furin inhibitor prevented infection by 682–686-deleted SARS-CoV-2 in 293T-ACE2-furin cells, but not the K814A mutant. K814A mutation did not affect the activity of TMPRSS2 and cathepsin L but did impact the cleavage of S2 into S2′ and cell–cell fusion. Additionally, we showed that this functional furin site exists in RaTG13 from bat and PCoV-GD/GX from pangolin. Therefore, we discovered a new functional furin site that is pivotal in promoting SARS-CoV-2 infection.

A simpler and user-friendly nucleic acid sensing platform with 10 aM sensitivity, named USPCRP (Combines the ultrashort PCR with Pyrococcus furiosus Argonaute cleavage for nuleic acids detection), among which the product of ultrashort PCR could be used as DNA guide directly to mediate PfAgo cleaving molecular beacons.

A sulfonium ylide participated alkylation and arylation under transition-metal free conditions is described. The disparate reaction pattern allowed the separate activation of non-ylidic S-alkyl and S-aryl bond. Under acidic conditions, sulfonium ylides serve as alkyl cation precursors which facilitate the alkylations. While under alkaline conditions, cleavage of non-ylidic S-aryl bond produces O-arylated compounds efficiently. The robustness of the protocols were established by the excellent compatibility of wide variety of substrates including carbohydrates.

2-Pyridinylmethyl Borrowing: Transition-metal-free 2-pyridinylmethyl borrowing C-alkylation of alcohols access to ketones is developed. This unstrained C(sp3)–C(sp3) bonds cleavage of unactivated alcohols avoids the use of transition metals.

A BF3•OEt2 catalyzed highly chemoselective formal C=C double bond cleavage reaction of α,β-enones with diazoamides for the synthesis of 3-alkylated oxindoles is developed. Boron trifluoride etherate is found to be an effective catalyst for the chemoselective Cα-Cβ cleavage of enones to achieve the 3-alkylated oxindoles. The product formation indicates a selective β-carbon elimination pathway of α,β-enones using inexpensive BF3•OEt2 as a catalyst, transition metal-free conditions, an open-air environment, good functional tolerance and broad substrate scope. The synthetic utility of this protocol is highlighted by synthesizing spiro-indolooxiranes.

Background: The CRISPR system can quickly achieve the editing of different gene loci by changing a small sequence on a single guide RNA. But the off-target event limits the further development of the CRISPR system. How to improve the efficiency and specificity of this technology and minimize the risk of off-target have always been a challenge. For genome-wide CRISPR Off-Target Cleavage Sites (OTS) prediction, an important issue is data imbalance, that is, the number of true OTS identified is much less than that of all possible nucleotide mismatch loci. Method: In this work, based on the sequence-generating adversarial network (SeqGAN), positive offtarget sequences were generated to amplify the off-target gene locus OTS dataset of Cpf1. Then we trained the data by a deep Convolutional Neural Network (CNN) to obtain a predictor with stronger generalization ability and better performance. Results: In 10-fold cross-validation, the AUC value of the CNN classifier after SeqGAN balance was 0.941, which was higher than that of the original 0.863 and over-sampling 0.929. In independence testing, the AUC value of the CNN classifier after SeqGAN balance was 0.841, which was higher than that of the original 0.833 and over-sampling 0.836. The PR value was 0.722 after SeqGAN, which was also about higher 0.16 than the original data and higher about 0.03 than over-sampling. Conclusion: The sequence generation antagonistic network SeqGAN was firstly used to deal with data imbalance processing on CRISPR data. All the results showed that the SeqGAN can effectively generate positive data for CRISPR off-target sites.

Fluorophores with different emission wavelengths were efficiently quenched by tert-butyl terminated tetrazylmethyl group and activated by isonitrile-tetrazine click-to-release reaction. Nucleic acid templated chemistry significantly accelerated this bioorthogonal cleavage. Moreover, two mutually orthogonal fluorogenic cleavage reactions were simultaneously conducted in live cells for the first time.

Although Ag catalysts have potential for 5-hydroxymethylfurfural (HMF) oxidation to 5-hydroxymethyl-2-furancarboxylic acid (HMFCA), further oxidation into 2,5-furandicarboxylic acid (FDCA) remains a severe challenge. Herein, we propose a strategy to synthesize CoOx–Ag/CeO2 catalysts where Ag+–Ov–Ce3+ interfacial sites are generated. For the first time, a mono-noble metal Ag catalyst, namely, CoOx–Ag/CeO2-2, achieves a satisfactory FDCA yield of 92.8%. Even under base-free conditions, a yield of 71.2% could still be obtained. A combination study unveils the harmonious cooperation between Ag+ and Ov–Ce3+ sites during the rate-determining step: the Ag+ site facilitates cleavage of the C–H bond, and the Ov–Ce3+ site enhances the adsorption of reactants and accelerates the dissociation of H2O and the transformation of the adsorbed O2 into superoxide radicals. The present work sheds light on the mechanism study on the HMF oxidation over Ag-based catalysts and may contribute to the rational design of high-performance heterogeneous catalysts.

Hedgehog (Hh) signaling ligands undergo carboxy terminal sterylation through specialized autoprocessing, called cholesterolysis. Sterylation is brought about intramolecularly in a single turn-over by an enzymatic domain, called HhC. HhC is found in precursor Hh proteins only. Through cholesterolysis, HhC is cleaved from the precursor. Attempts to identify molecules that inhibit intramolecular cleavage/sterylation activity of HhC have resulted in antagonists that bind HhC irreversibly through covalent mechanisms, as is commonplace for protein autoprocessing inhibitors. Here we report an exception to the “irreversibility rule” for protein autoprocessing inhibition. Using a FRET-based activity assay for HhC, we screened a focused library of sterol-like analogs for HhC cholesterolysis inhibitors. We identified and validated four structurally related noncovalent inhibitors, which were then used for SAR studies. The most effective derivative, tBT-HBT, binds HhC reversibly with an IC50 of 300 nM. An allosteric binding site for tBT-HBT, encompassing interactions from the two subdomains of HhC, is suggested by kinetic analysis, mutagenesis studies, and photoaffinity labeling. A striking resemblance is found between the inhibitors described here and a family of noncovalent, allosteric activators of HhC, which we described previously. The inhibitor/activator duality appears to be mediated by the same allosteric site, which displays sensitivity to subtle differences in the structure of a heterocycle substituent on the effector molecule.

Antibody-drug conjugates (ADCs) are a rapidly emerging therapeutic platform. The chemical linker between the antibody and the drug payload plays an essential role in the efficacy and tolerability of these agents. New methods that quantitively assess cleavage efficiency in complex tissue settings could provide valuable insights into the ADC design process. Here we report the development of a near-infrared (NIR) optical imaging approach that measures the site and extent of linker cleavage in mouse models. This approach is enabled by a superior variant of our recently devised cyanine carbamate (CyBam) platform. We identify a novel tertiary amine-containing norcyanine, the product of CyBam cleavage, that exhibits dramatically in-creased cellular signal due to improved cellular permeability and lysosomal accumulation. The resulting cyanine lysosome-targeting carbamates (CyLBams) are ~50X brighter in cells, and we find this strategy is essential for high-contrast in vivo targeted imaging. Finally, we compare a panel of several common ADC linkers across two antibodies and tumor models. These studies indicate that cathepsin-cleavable linkers provide dramatically higher tumor activation relative to hindered or non-hindered disulfides – an observation that is only apparent with in vivo imaging. This strategy enables quantitative comparisons of cleavable linker chemistries in complex tissue settings with implications across the drug delivery landscape.

Hepatitis B virus (HBV) uses e antigen (HBe), which is dispensable for virus infectivity, to modulate host immune responses and achieve viral persistence in human hepatocytes. The HBe precursor (p25) is directed to the endoplasmic reticulum (ER), where cleavage of the signal peptide (sp) gives rise to the first processing product, p22. P22 can be retro-translocated back to the cytosol or enter the secretory pathway and undergo a second cleavage event, resulting in secreted p17 (HBe). Here, we report that translocation of p25 to the ER is promoted by translocon-associated protein complex (TRAP). We have found that p25 is not completely translocated into the ER; a fraction of p25 is phosphorylated and remains in the cytoplasm and nucleus. Within the p25 sp sequence, we have identified three cysteine residues that control the efficiency of sp cleavage and contribute to proper subcellular distribution of the precore pool.

This paper presents a probe comprising a fluorophore and a quencher, enabling measurement of released product from self-cleaving hammerhead ribozyme, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two DNA strands; one strand is labeled with a fluorophore at its 5′-end, while the other strand is labeled with a quencher at its 3′-end. These two DNA strands are perfectly complementary, but with a 3′-overhang of the fluorophore strand. These unpaired nucleotides act as a toehold, which is utilized by a detached cleaved fragment (coming from a self-cleaving hammerhead ribozyme) as the starting point for a strand displacement reaction. This reaction causes the separation of the fluorophore strand from the quencher strand, culminating in fluorescence, detectable in a plate reader. Notably, the emitted fluorescence is proportional to the amount of detached cleaved-off RNAs, displacing the DNA quencher strand. This method can replace or complement radio-hazardous unstable 32P as a method of measurement of the product release from ribozyme cleavage reactions; it also eliminates the need for polyacrylamide gels, for the same purpose. Critically, this method allows to distinguish between the total amount of cleaved ribozymes and the amount of detached fragments, resulting from that cleavage reaction.

SQSTM1/p62, as a major autophagy receptor, forms droplets that are critical for cargo recognition, nucleation, and clearance. p62 droplets also function as liquid assembly platforms to allow the formation of autophagosomes at their surfaces. It is unknown how p62-droplet formation is regulated under physiological or pathological conditions. Here, we report that p62-droplet formation is selectively blocked by inflammatory toxicity, which induces cleavage of p62 by caspase-6 at a novel cleavage site D256, a conserved site across human, mouse, rat, and zebrafish. The N-terminal cleavage product is relatively stable, whereas the C-terminal product appears undetectable. Using a variety of cellular models, we show that the p62 N-terminal caspase-6 cleavage product (p62-N) plays a dominant-negative role to block p62-droplet formation. In vitro p62 phase separation assays confirm this observation. Dominant-negative regulation of p62-droplet formation by caspase-6 cleavage attenuates p62 droplets dependent autophagosome formation. Our study suggests a novel pathway to modulate autophagy through the caspase-6–p62 axis under certain stress stimuli.

We have shown previously that exposing bacteria to tetrachlorocatechol (TCC) and sodium azide (NaN3) together causes synergistic cytotoxicity in a biphasic mode. However, the underlying chemical mechanism remains unclear. In this study, an unexpected ring-contraction 3(2H)-furanone and two quinoid-compounds were identified as the major and minor reaction products, respectively; and two unusual azido-substituted chloro-O-semiquinone radicals were detected and characterized as the major radical intermediates by complementary applications of direct ESR, HPLC/ESI-Q-TOF and high-resolution MS studies with nitrogen-15 isotope-labeled NaN3. Taken together, we proposed a novel molecular mechanism for the reaction of TCC/NaN3: N3- may attack on tetrachloro-O-semiquinone radical, forming two transient 4-azido-3,5,6-trichloro- and 4,5-diazido-3,6-dichloro-O-semiquinone radicals, consecutively. The second-radical intermediate may either undergo an unusual zwitt-azido cleavage to form the less-toxic ring-contraction 3(2H)-furanone product, or further oxidize to form the more toxic quinoid-product 4-amino-5-azido-3,6-dichloro-O-benzoquinone. A good correlation was observed between the biphasic formation of this toxic quinone due to the two competing decomposition pathways of the radical intermediate and the biphasic synergism between TCC and NaN3, which are dependent on their molar-ratios. This is the first report of detection and identification of two unique azido-substituted chloro-O-semiquinone radicals, and an unprecedented ring-contraction mechanism via an unusually mild and facile zwitt-azido rearrangement.

Selective detection of multiple analytes in a compact design with dual-modality and theranostic features presents great challenges. Herein, we wish to report a coumarin-thiazolidine masked D -penicillamine based dual-modality fluorescent probe COU-DPA-1 for selective detection, differentiation, and detoxification of multiple heavy metal ions (Ag+, Hg2+, Cu2+). The probe shows divergent fluorescence (FL) /circular dichroism (CD) responses via divergent bond-cleavage cascade reactions (metal ion promoted C-S cleavage and hydrolysis at two distinctive cleavage sites): FL “turn-off” and CD “turn-on” for Ag+ (no hydrolysis), FL “turn-on” and CD “turn-off” for Hg2+ (imine hydrolysis), and FL “self-threshold ratiometric” and CD “turn-off” for excess Cu2+ (lactone and imine hydrolysis), providing the first example of a fluorescence/CD dual-modality probe for multiple species with complimentary responses. Moreover, the bond-cleavage cascade reactions also lead to the formation of D -penicillamine heavy metal ion complexes for potential detoxification treatments.

We used MALDI-MS to study the interaction of amyloid β (Aβ) peptides with alpha-2-macroglobulin (α2M). The binding of amyloid beta (Aβ) peptides to alpha-2-macroglobulin (α2M) was found to inhibit the ability of trypsin to cleave out the peptide α2M 705–715 (Pep-α2M) from α2M. This was observed with both purified α2M and α2M in human serum. We found that Aβ 1–38, Aβ1-40, and Aβ 1–42, all inhibit the interaction of α2M with trypsin, with inhibition rate independent of the length of the Aβ peptide. Further, we show that for complete inhibition, two peptide molecules must be attached to one α2M molecule; one for each of its two subunits. A region was revealed within the Aβ sequence, in which proteolytic cleavage (Lys-28) and oxidation (Met-35) lead to a loss of their ability to inhibit the interaction of trypsin with α2M. Furthermore, we show that after the formation of a trypsin complex with α2M and cleavage of α2M to produce the α2M 705–715, Aβ peptides continue to bind to the protein in the same proportions. However, Aβ peptides treated with DMSO lost their ability to bind to α2M and thereby to inhibit the interaction of trypsin with α2M. While maintaining their primary structure, such an effect can be explained only by conformational changes in the peptides, suggesting the possibility to use our analytical approach to distinguish between conformational isomers of Aβ peptides.

Airway epithelial cells are the first line of defense against respiratory pathogens. Porcine bacterial pathogens, such as Bordetella bronchiseptica, Actinobacillus pleuropneumoniae, Glaesserella (Haemophilus) parasuis, and Pasteurella multocida, breach this barrier to lead to local or systematic infections. Here, we demonstrated that respiratory bacterial pathogen infection disrupted the airway epithelial intercellular junction protein, E-cadherin, thus contributing to impaired epithelial cell integrity. E-cadherin knocking-out in newborn pig tracheal cells via CRISPR/Cas9 editing technology confirmed that E-cadherin was sufficient to suppress the paracellular transmigration of these porcine respiratory bacterial pathogens, including G. parasuis, A. pleuropneumoniae, P. multocida, and B. bronchiseptica. The E-cadherin ectodomain cleavage by these pathogens was probably attributed to bacterial HtrA/DegQ protease, but not host HtrA1, MMP7 and ADAM10, and the prominent proteolytic activity was further confirmed by a serine-to-alanine substitution mutation in the active center of HtrA/DegQ protein. Moreover, deletion of the htrA gene in G. parasuis led to severe defects in E-cadherin ectodomain cleavage, cell adherence and paracellular transmigration in vitro, as well as bacterial breaking through the tracheal epithelial cells, systemic invasion and dissemination in vivo. This common pathogenic mechanism shared by other porcine respiratory bacterial pathogens explains how these bacterial pathogens destroy the airway epithelial cell barriers and proliferate in respiratory mucosal surface or other systemic tissues.

Structural binary cleavage of 3,7-diamino-2,6-dinitro-1H,5H-pyrazolo-[1,2-a]pyrazole-1,5-dione 3, under nucleophilic conditions, leads to the formation of a monocyclic pyrazole unit of 5-amino-4-nitro-1,2-dihydro-3H-pyrazol-3-one, 4. Additionally, various salts of the pyrazole ring were synthesized and fully characterized. Detonation properties and mechanical sensitivities of 4 and other new compounds are remarkably improved compared to 3. This simple and efficient strategy is highly desirable for future studies on the development of insensitive and high performing materials.

Studies have demonstrated that PE_PGRS45 is constitutively expressed under various environmental conditions (such as nutrient depletion, hypoxia, and low pH) of the in vitro growth conditions examined, indicating that PE_PGRS45 protein is critical to the basic functions of M.tuberculosis. However, there are few reports about the biochemical function and pathogenic mechanism of PE_PGRS45 protein. The fact that the gene of M. tuberculosis is not easily expressed in E. coli may be mainly due to the high content of G+C and the use of unique codons. Fusion tags are indispensable tools used to improve the soluble expression of recombinant proteins and accelerate the characterization of protein structure and function. In the present study, His6, Trx, His6-MBP were used as fusion tags, but only MBP-PE_PGRS45 formed expressed solubly. The purification using His6-MBP tag specific binding to the Ni column and is easy to separate after the tag cleavage. We used the purified PE_PGRS45 to immunize New Zealand rabbits and got the serum of anti PE_PGRS45. It was found that the titer of polyclonal antibodies against PE_PGR45 was higher than 1:256000. The result shows that the purified PE_PGRS45 can induce New Zealand rabbits to produce high titer antibodies. In conclusion, the recombinant protein PE_PGRS45 was successfully expressed in E. coli and specific antiserum was prepared, which will be followed by further evaluation of these specific antigens to develop highly sensitive and specific diagnostic tests for tuberculosis.

Streptococcus pyogenes Cas9 (SpCas9), a programmable RNA-guided DNA endonuclease, has been widely repurposed for biological and medical applications. Critical interactions between SpCas9 and DNA confer the high specificity of the enzyme in genome engineering. Here, we unveil that an essential SpCas9–DNA interaction located beyond the protospacer adjacent motif (PAM) is realized through electrostatic forces between four positively charged lysines among SpCas9 residues 1151–1156 and the negatively charged DNA backbone. Modulating this interaction by substituting lysines with amino acids that have distinct charges revealed a strong dependence of DNA target binding and cleavage activities of SpCas9 on the charge. Moreover, the SpCas9 mutants show markedly distinguishable DNA interaction sites beyond the PAM compared with wild-type SpCas9. Functionally, this interaction governs DNA sampling and participates in protospacer DNA unwinding during DNA interrogation. Overall, a mechanistic and functional understanding of this vital interaction explains how SpCas9 carries out efficient DNA interrogation.

The complex physical and chemical interactions between DNA and 0-3 eV electrons released by UV photoionization can lead to the formation of various lesions such as base modifications and cleavage, crosslinks and single strand breaks. Furthermore, in the presence of platinum chemotherapeutic agents, these electrons can cause clustered lesions, including double strand breaks. We explain the mechanisms responsible for these damages via the production 0-3 eV electrons by UVC radiation, and by UV photons of any wavelengths, when they are produced by photoemission from nanoparticles lying within about 10 nm from DNA. We review experimental evidence showing that a single 0-3 eV electron can produce these damages. The foreseen benefits UV-irradiation of nanoparticles targeted to the cell nucleus are mentioned in the context of cancer therapy, as well as the potential hazards to human health when they are present in cells.

PURPOSE: This study was conducted to verify if the cfDNA integrity (cfDI) in follicular fluid and subsequent spent embryo medium (SEM) could serve as potential non-invasive biomarker for high-grade embryo selection during IVF/ICSI. METHODS: Thirty-two follicular fluids, 32 subsequent corresponding cleavage embryo SEM, and 23 subsequent blastocyst SEM were collected from 11 patients undergoing IVF/ICSI. CfDI was measured by ALU gene amplicons with different sizes by qPCR, as the ratio of long to short fragments. RESULTS: CfDI in follicular fluid corresponding to subsequent high-grade cleavage embryos and blastocysts was significantly lower than that related to low-grade embryos (p = 0.018). Conversely, cfDI in SEM was significantly and positively correlated with high-grade embryos at both stages (p = 0.009). ROC curves of the analysis of cfDI in follicular fluid showed great potential in predicting subsequent embryogenesis and embryo grade (AUC > 0.927). Regardless of the cleavage embryo grade by morphology, cfDI in day 3 SEM could predict if the cleavage embryo could develop to a high-grade blastocyst (AUC = 0.820). A concordant shift pattern of cfDI from follicular fluid to subsequent day 3 SEM and day 5 SEM was found in 81.82% participants featured by various clinical characteristics. CONCLUSION: CfDI in follicular fluid and SEM was significantly correlated with embryogenesis and embryo grade and could serve as a potential non-invasive biomarker in high-grade embryo selection. Direct qPCR was proved as a labor-saving and sensitive method for the analysis of cfDI in low volume of SEM. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10815-021-02357-0.

The dehydroacylation of ketones to olefins is realized under mild conditions, which exhibits a unique reaction pathway involving aromatization-driven C–C cleavage to remove the acyl moiety, followed by Cu-mediated oxidative elimination to form an alkene between the α and β carbons. The newly-adopted N’-methylpicolinohydrazonamide (MPHA) reagent is key to enable efficient cleavage of ketone C–C bonds at room temperature. Diverse alkyl- and aryl-substituted olefins, dienes, and special alkenes are generated with broad functional group tolerance. Strategic applications of this method are also demonstrated.

Lignin is the most abundant natural, aromatic-containing biopolymer. Among all the C–C and C–O bonds being cleaved in catalytic fractionation, the 5–5 linkage is the strongest, and its scission req...

RNA-cleaving DNAzymes and their multicomponent nucleic acid enzymes (MNAzymes) have been successfully used to detect nucleic acids and proteins. The appropriate split of the catalytic cores of DNAzymes is critical to the formation of MNAzymes with high catalytic activities. However, for protein detection, no systematic investigation has been made on the effects of the split locations and secondary structures of MNAzymes on the catalytic activities of the cleavage reaction. We systematically studied how split locations and secondary structures affect the activity of the MNAzymes that catalyze multiple cleavage steps. We engineered the MNAzymes on the basis of the RNA-cleaving DNAzyme 10-23 as a model system. We designed 28 pairs of MNAzymes, representing 14 different split locations and two secondary structures: the three-arm and the four-arm structures. By comparing the multiple turnover numbers (kobs.m) of the 28 MNAzymes, we showed that the split location between the seventh cytosine and the eighth thymine of the catalytic core region and the four-arm structure resulted in optimum catalytic activity. Binding-induced DNA assembly of the optimized MNAzymes enabled sensitive detection of two model protein targets, demonstrating promising potential of the binding-assembled MNAzymes for protein analysis. The strategy of binding-assembled MNAzymes and systematic studies measuring multiple turnover numbers (kobs.m) provide a new approach to studying other partial (split) DNAzymes and engineering better MNAzymes for the detection of specific proteins.

A mechanism study for Pd(II)-catalyzed C(sp3)-H activation using a self-cleaving chlorotetrafluoroethylsulfinyl (-SOCF2CF2Cl) auxiliary as a directing group is reported. Mechanistic studies reveal that (1) the auxiliary group is crucial for C(sp3)-H activation, (2) the reaction undergoes a C(sp3)-H olefination-Michael addition-removal of the auxiliary sequence, (3) the removal of the auxiliary (SORf) is most likely the alcoholic solvolysis of the -SOCF2CF2Cl group on the N-tri-substituted sulfonamides, and (4) the C(sp3)-H cleavage is involved in the rate-determining step.

A facile method is disclosed for the synthesis of α-thio/selenocyanato ketones through regioselective C-H thio/selenocyanation of ketones. The advantages include the use of easily available starting materials, high efficiency, simple operation, and easy scale-up. Control experiments provide evidence that the reaction proceeded via a radical way, while kinetic isotope effect experiments reveal that the cleavage of the C-H bond serves as the rate-limiting step.

Iron-catalyzed direct SN2' dehydroxyboration of allylic alcohols has been developed to access (E)-stereoselective allylboronates. Allylic alcohols with diverse structures and functional groups, especially derived from natural products, underwent smooth transformation. The six-membered ring transition state formed by allylic alcohols and iron-boron intermediate was indicated to be the key component involved in transfer of the boron group, activation of the C-OH bond, and control of the stereoselectivity.

A direct cross-coupling between 9H-fluoren-9-ols and organic azides for the synthesis of steric hindered 2-amino-2'-ketonyl biaryls was reported. The reaction featured an acid-mediated azidation/ring-expansion/hydrolysis cascade, which formally realized the C-N bond coupling reaction via cleavage of a C-C single bond. This method was applicable to chiral helical structure to give bulky axially chiral biaryls with full stereospecificity.

CRISPR-Cas systems are RNA-guided nucleases that provide adaptive immune protection in bacteria and archaea against intruding genomic materials. Cas9, a type-II CRISPR effector protein, is widely used for gene editing applications since a single guide RNA can direct Cas9 to cleave specific genomic targets. The conformational changes associated with RNA/DNA binding are being modulated to develop Cas9 variants with reduced off-target cleavage. Previously, we showed that proline substitutions in the arginine-rich bridge helix (BH) of Streptococcus pyogenes Cas9 (SpyCas9-L64P-K65P, SpyCas92Pro) improve target DNA cleavage selectivity. In this study, we establish that kinetic analysis of the cleavage of supercoiled plasmid substrates provides a facile means to analyze the use of two parallel routes for DNA linearization by SpyCas9: (i) nicking by HNH followed by RuvC cleavage (the TS (target strand) pathway) and (ii) nicking by RuvC followed by HNH cleavage (the NTS (nontarget strand) pathway). BH substitutions and DNA mismatches alter the individual rate constants, resulting in changes in the relative use of the two pathways and the production of nicked and linear species within a given pathway. The results reveal coordinated actions between HNH and RuvC to linearize DNA, which is modulated by the integrity of the BH and the position of the mismatch in the substrate, with each condition producing distinct conformational energy landscapes as observed by molecular dynamics simulations. Overall, our results indicate that BH interactions with RNA/DNA enable target DNA discrimination through the differential use of the parallel sequential pathways driven by HNH/RuvC coordination.

The ability of RNA to catalyze RNA ligation is critical to its central role in many prebiotic model scenarios, in particular the copying of information during self-replication. Prebiotically plausible ribozymes formed from short oligonucleotides can catalyze reversible RNA cleavage and ligation reactions, but harsh conditions or unusual scenarios are often required to promote folding and drive the reaction equilibrium towards ligation. Here, we demonstrate that ribozyme activity is greatly enhanced by charge-mediated phase separation with poly-L-lysine, which shifts the reaction equilibrium from cleavage in solution to ligation in peptide-RNA coaggregates and coacervates. This compartmentalization enables robust isothermal RNA assembly over a broad range of conditions, which can be leveraged to assemble long and complex RNAs from short fragments under mild conditions in the absence of exogenous activation chemistry, bridging the gap between pools of short oligomers and functional RNAs., Angew. Chem., Int. Ed. Engl.;60(50)

Herein, we report a protocol for PtI2-catalyzed formal three-component cascade cycloaddition reactions between γ-aminoalkynes and electron-deficient alkynes to afford highly substituted cyclohexadiene-b-pyrrolidines in good yields. On the basis of the results of the control experiments and density functional theory calculations, we present a plausible mechanism that proceeds via two key intermediates. The overall transformation involves the cleavage and formation of multiple C-C and C-N bonds and a previously unreported reaction mode of a seven-membered nitrogen heterocyclic intermediate.

Self-immolative polymers (SIPs) are characterized by their ability to depolymerize in response to the cleavage of a single end-cap or backbone moiety, making them attractive for numerous applicatio...

The results of this study show that disilathiane is an effective mediator in the synthesis of alkyl aryl sulfides with disulfides and alkyl carboxylates. Mechanistic studies suggest that disilathiane promotes cleavage of the sulfur-sulfur bond of disulfides to generate thiosilane as a key intermediate. Diselenides were also applicable to this transformation to produce the corresponding selenides.

Innovation of high-value added lignin derivatives has become a topic of interest, but lignin modification and utilization remain a challenge due to lignin’s complicated structure. In our previous study, we successfully improved water resistance and adhesion performance of soy protein adhesives using unmodified lignin. This study focuses on lignin modification as well as lignin-protein properties and interactions. Lignin modification was achieved by pH changes and pH-shifting. Cleavage of β-O-4 linkage was observed at pH 8.5 and pH 12, resulting in smaller particle sizes and changes in thermal properties. Partial repolymerization was found after pH-shifting treatments. Lignin increased the strength of protein films under high temperature and significantly enhanced the water resistance of soy protein at pH 12. Cross-linking of protein and lignin took place via carbonyl, amino, and hydroxyl groups. Multiple-point interactions between lignin and protein resulted in a stronger lignin-protein network. Additional lignin-protein complexes with high molecular weight were detected with an elevated lignin concentration at pH 8.5. The binding interaction between lignin and protein, although of non-specific nature, was also observed by isothermal titration calorimetry (ITC). Findings of this study contribute to the further development of green lignin-protein products.

A new [PCCP]-coordinated molybdenum platform comprising a coordinated alkyne was employed for the cleavage of molecular dinitrogen. The coordinated η2 -alkyne was left unaffected during this reduction. DFT calculations suggest that the reaction proceeds via an initially generated terminal N2 -complex, which is converted to a dinuclear μ-(η1 :η1 )-N2 -bridged intermediate prior to N-N bond cleavage. Protonation, alkylation and acylation of the resulting molybdenum nitrido complex led to the corresponding N-functionalized imido complexes. Upon oxidation of the N-acylated imido derivative in MeCN, a fumaronitrile fragment was built up via C-C coupling of MeCN to afford a dinuclear molybdenum complex. The key finding that the strong N≡N bond may be cleaved in the presence of a weaker, but spatially constrained C≡C bond contradicts the widespread paradigm that coordinated alkynes are in general more reactive than gaseous N2 .

The autosomal dominant striated muscle disease myoglobinopathy is due to the single point mutation His98Tyr in human myoglobin (MB) [Olive et al. (2019) Nat Comm 10, 1396], the heme protein responsible for binding, storage, and controlled release of O2 in striated muscle. In order to understand the molecular basis of this disease, a comprehensive biochemical and biophysical study on wt MB and the variant H98Y has been performed. Although only small differences exist between the active site architectures of the two proteins, the mutant (a) exhibits an increased reactivity toward hydrogen peroxide, (b) exhibits a higher tendency to form high-molecular-weight aggregates, and (c) is more prone to heme bleaching, possibly as a consequence of the observed H2 O2 -induced formation of the Tyr98 radical close to the metal center. These effects add to the impaired oxygen binding capacity and faster heme dissociation of the H98Y variant compared with wt MB. As the above effects result from bond formation/cleavage events occurring at the distal and proximal heme sites, it appears that the molecular determinants of the disease are localized there. These findings set the basis for clarifying the onset of the cascade of chemical events that are responsible for the pathological symptoms of myoglobinopathy.

The mechanisms of hydroxyl radical (·OH) degradation of disperse red 73 (DR73) dye were investigated using density functional theory (DFT) calculations. Comparative feasibility of ·OH attack at the azo (N=N) site or on a > C–N group was examined based on their energies with a view to determine the more preferred pathway for DR73 degradation and predict its degradation products. Further decomposition of the cleavage products by ·OH radical through processes such as deamination and loss of molecular nitrogen was also examined. The results showed that ·OH radical attack on DR73 is more favourable via the azo (N=N) site. However, subsequent rupture of the N=N bond was found to be kinetically and thermodynamically less favourable compared to the C–N bond rupture arising from the attack of the radical on a ring carbon attached to the azo group. Introduction of water (as a solvent) was found to produce an accelerating and stabilising effects on the N=N bond cleavage mechanism, but an inhibitory and destabilising effects on the C–N counterpart. Deamination and nitrogen evolution reactions of the primary degradation products upon further ·OH radical attack were found to be kinetically and thermodynamically feasible.

Pyroptosis is a highly inflammatory and lytic type of programmed cell death (PCD) commenced by inflammasomes, which sense perturbations in the cytosolic environment. Recently, several ground-breaking studies have linked a family of pore-forming proteins known as gasdermins (GSDMs) to pyroptosis. The human genome encodes six GSDM proteins which have a characteristic feature of forming pores in the plasma membrane resulting in the disruption of cellular homeostasis and subsequent induction of cell death. GSDMs have an N-terminal cytotoxic domain and an auto-inhibitory C-terminal domain linked together through a flexible hinge region whose proteolytic cleavage by various enzymes releases the N-terminal fragment that can insert itself into the inner leaflet of the plasma membrane by binding to acidic lipids leading to pore formation. Emerging studies have disclosed the involvement of GSDMs in various modalities of PCD highlighting their role in diverse cellular and pathological processes. Recently, the cryo-EM structures of the GSDMA3 and GSDMD pores were resolved which have provided valuable insights into the pore formation process of GSDMs. Here, we discuss the current knowledge regarding the role of GSDMs in PCD, structural and molecular aspects of autoinhibition, and pore formation mechanism followed by a summary of functional consequences of gasdermin-induced membrane permeabilization.