Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis

DNA Reaction Networks Composed of Standardized Switchable Molecular Devices for Recording Temporal Molecular Events

The processing of temporal information plays a key supporting role in accurately perceiving molecular dynamic changes and making complex molecular decisions. As such, the development of artificial molecular networks that can efficiently process and record temporal molecular events (TMEs) has high scientific and practical value. Among them, DNA reaction networks (DRNs) have opened up an avenue for processing molecular temporal information, owing to their outstanding advantages. Therefore, we developed a standardized switchable molecular device, which is used to build DRNs that can handle temporal information on multiple types of biomolecules. Standardized molecular devices allow rapid network assembly, and their efficient state switching affords flexibility to the networks. The experimental findings show that the collaborative state switching network (CSSN) and cross-inhibition network (CIN) built from these molecular devices not only possess temporal resolution for DNA molecular events (MEs) but also show time sensitivity over specific time spans. Taking two microRNAs (miRNAs) as research subjects further confirms the temporal resolution ability of the CIN. Moreover, through an extended CIN, the perception of the temporal sequence of two proteins was realized, highlighting the proposed DRNs' application potential in fields including molecular information processing, biosensing, and disease diagnosis and treatment.

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2

The importance of Mg2+ ions for RNA structure and function cannot be overstated. Several attempts were made to establish a comprehensive Mg2+ binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites as observed in a recent cryo-EM 1.55 Å Escherichia coli ribosome structure where incomplete ion assignments blurred our understanding of their binding patterns. We revisited this model to establish general binding principles applicable to any RNA of sufficient resolution. These principles rely on the 2.9 Å distance separating two water molecules bound in cis to Mg2+. By applying these rules, we could assign all Mg2+ ions bound with 2-4 non-water oxygens. We also uncovered unanticipated motifs where up to five adjacent nucleotides wrap around a single ion. The formation of such motifs involves a hierarchical Mg2+ ion dehydration process that plays a significant role in ribosome biogenesis and in the folding of large RNAs. Besides, we established a classification of the Mg2+…Mg2+ and Mg2+…K+ ion pairs observed in this ribosome. Overall, the uncovered binding principles enhance our understanding of the roles of ions in RNA structure and will help refining the solvation shell of other RNA systems.

Concurrent manipulation of competitive mechanisms to construct glutathione-stabilized gold nanocluster-based dual-channel molecular classifier for metal ions detection and information steganography

Understanding charge transport in metal ion-mediated glutathione-stabilized gold nanoclusters (GSH-Au NCs) has proved difficult due to the presence of various competitive mechanisms, such as electron transfer (ET) and aggregation induction effect (AIE). In this paper, we present a dual-channel fluorescence (FL) and second-order Rayleigh scattering (SRS) sensing method for high-throughput classification of metal ions, relying on the competition between ET and AIE using GSH-Au NCs. The SRS signals show significant enhancement when Pb2+, Ag+, Al3+, Cu2+, Fe3+, and Hg2+ are present, as a result of the aggregation of GSH-Au NCs. Notably, the fluorescence signal exhibits the opposite trend. The FL intensities of GSH-Au NCs are enhanced by Pb2+, Ag+, and Al3+ through the AIE mechanism, while they are quenched by Cu2+, Fe3+, and Hg2+, which is dominated by the ET mechanism. By employing principal component analysis and hierarchical cluster analysis, these signals are transformed into unique fingerprints and Euclidean distances, respectively, enabling successful distinction of six metal ions and their mixtures with a low detection limit of 30 nM. This new strategy has successfully addressed interference from impurities in the testing of real water samples, demonstrating its strong ability to detect multiple metal ions. Impressively, we have achieved molecular cryptosteganography, which involves encoding, storing, and concealing information by transforming the selective response of GSH-Au NCs to binary strings. This research is anticipated to advance utilization of nanomaterials in logic sensing and information safety, bridging the gap between molecular sensors and information systems.

Inhibitory interactions of the 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one scaffold with Bunyavirales cap-snatching endonucleases expose relevant drug design features

The World Health Organization (WHO) identifies several bunyaviruses as significant threats to global public health security. Developing effective therapies against these viruses is crucial to combat future outbreaks and mitigate their impact on patient outcomes. Here, we report the synthesis of some isoindol-1-one derivatives and explore their inhibitory properties over an indispensable metal-dependent cap-snatching endonuclease (Cap-ENDO) shared among evolutionary divergent bunyaviruses. The compounds suppressed RNA hydrolysis by Cap-ENDOs, with IC50 values predominantly in the lower μM range. Molecular docking studies revealed the interactions with metal ions to be essential for the 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one scaffold activity. Calorimetric analysis uncovered Mn2+ ions to have the highest affinity for sites within the targets, irrespective of aminoacidic variations influencing metal cofactor preferences. Interestingly, spectrophotometric findings unveiled sole dinuclear species formation between the scaffold and Mn2+. Moreover, the complexation of two Mn2+ ions within the viral enzymes appears to be favourable, as indicated by the binding of compound 11 to TOSV Cap-ENDO (Kd = 28 ± 3 μM). Additionally, the tendency of compound 11 to stabilize His+ more than His- Cap-ENDOs suggests exploitable differences in their catalytic pockets relevant to improving specificity. Collectively, our results underscore the isoindolinone scaffold's potential as a strategic starting point for the design of pan-antibunyavirus drugs.

Programmable DNA barcode-encoded exponential amplification reaction for the multiplex detection of miRNAs

Multiple analysis of miRNAs is essential for the early diagnosis and monitoring of diseases. Here, a programmable, multiplex, and sensitive approach was developed for one-pot detection of miRNAs by melting temperature encoded sequences and exponential isothermal amplification (E-EXPAR). In the presence of target miRNAs, the corresponding templates initiate the cycles of nicking and polymerization/displacement, generating numerous barcode strands with unique encoding sequences. Subsequently, generated barcode strands hybridize with fluorescent probes and quench the fluorophore by a triplet of G base through a photo-induced electron transfer mechanism. Finally, a melting curve analysis is performed to quantify miRNAs by calculating the rate of fluorescence change at the corresponding melting temperature. Based on this, miRNA-21, miRNA-9, and miRNA-122 were detected with the detection limits of 3.3 fM, 2.9 fM, and 1.7 fM, respectively. This E-EXPAR was also employed to simultaneously detect three miRNAs in biological samples, showing consistent results with RT-qPCR. Overall, this study provides a programmable and universal platform for multiplex analysis of miRNAs, and holds great promise as an alternative to the multiplex analysis in clinical diagnostics and prognostics for nucleic acid detection.

A Proofreading Mutation with an Allosteric Effect Allows a Cluster of SARS-CoV-2 Viruses to Rapidly Evolve

The RNA-dependent RNA polymerase of the severe acute respiratory syndrome coronavirus 2 virus is error prone, with errors being corrected by the exonuclease (NSP14) proofreading mechanism. However, the mutagenesis and subsequent evolutionary trajectory of the virus is mediated by the delicate interplay of replicase fidelity and environmental pressures. Here, we have shown that a single, distal mutation (F60S) in NSP14 can have a profound impact upon proofreading with an increased accumulation of mutations and elevated evolutionary rate being observed. Understanding the implications of these changes is crucial, as these underlying mutational processes may have important implications for understanding the population-wide evolution of the virus. This study underscores the urgent need for continued research into the replicative mechanisms of this virus to combat its continued impact on global health, through the re-emergence of immuno-evasive variants.

Unwinding mechanism of SARS-CoV helicase (nsp13) in the presence of Ca2+, elucidated by biochemical and single-molecular studies

The recent outbreak of COVID-19 has created a serious health crisis with fatFal infectious viral diseases, such as Severe Acute Respiratory Syndrome (SARS). The nsp13, a helicase of coronaviruses is an essential element for viral replication that unwinds secondary structures of DNA and RNA, and is thus considered a major therapeutic target for treatment. The replication of coronaviruses and other retroviruses occurs in the cytoplasm of infected cells, in association with viral replication organelles, called virus-induced cytosolic double-membrane vesicles (DMVs). In addition, an increase in cytosolic Ca2+ concentration accelerates viral replication. However, the molecular mechanism of nsp13 in the presence of Ca2+ is not well understood. In this study, we applied biochemical methods and single-molecule techniques to demonstrate how nsp13 achieves its unwinding activity while performing ATP hydrolysis in the presence of Ca2+. Our study found that nsp13 could efficiently unwind double stranded (ds) DNA under physiological concentration of Ca2+ of cytosolic DMVs. These findings provide new insights into the properties of nsp13 in the range of calcium in cytosolic DMVs.

Bioinspired Active Site with a Coordination-Adaptive Organosulfonate Ligand for Catalytic Water Oxidation at Neutral pH

Many enzymes use adaptive frameworks to preorganize substrates, accommodate various structural and electronic demands of intermediates, and accelerate related catalysis. Inspired by biological systems, a Ru-based molecular water oxidation catalyst containing a configurationally labile ligand [2,2':6',2″-terpyridine]-6,6″-disulfonate was designed to mimic enzymatic framework, in which the sulfonate coordination is highly flexible and functions as both an electron donor to stabilize high-valent Ru and a proton acceptor to accelerate water dissociation, thus boosting the catalytic water oxidation performance thermodynamically and kinetically. The combination of single-crystal X-ray analysis, various temperature NMR, electrochemical techniques, and DFT calculations was utilized to investigate the fundamental role of the self-adaptive ligand, demonstrating that the on-demand configurational changes give rise to fast catalytic kinetics with a turnover frequency (TOF) over 2000 s^-1, which is compared to oxygen-evolving complex (OEC) in natural photosynthesis.

Construction of DNA-based molecular circuits using normally open and normally closed switches driven by lambda exonuclease

Building synthetic molecular circuits is an important way to realize ion detection, information processing, and molecular computing. However, it is still challenging to implement the NOT logic controlled by a single molecule input in synthetic molecular circuits wherein the presence or absence of the molecule represents the ON or OFF state of the input. Here, based on lambda exonuclease (λ exo), for the first time, we propose the normally open (NO) and normally closed (NC) switching strategy with a unified signal transmission mechanism to build molecular circuits. Specifically, the opposite logic can be output with or without a single signal, and the state of the switch can be adjusted by the addition order and time interval of the upstream signal and switch signal, which endows the switch with time-responsive characteristics. In addition, a time-delay relay with the function of delayed disconnection is developed to realize quantitative control of outputs, which has the potential to meet the automation control need of the system. Finally, digital square and square root circuits are constructed by cascading the NO and NC switches, which demonstrates the versatility of switches. Our design can be extended to time logic and complex digital computing circuits for use in information processing and nanomachines.

Discrete RNA-DNA hybrid cleavage by the EXD2 exonuclease pinpoints two rate-limiting steps

EXD2 is a recently identified exonuclease that cleaves RNA and DNA in double-stranded (ds) forms. It thus serves as a model system for investigating the similarities and discrepancies between exoribonuclease and exodeoxyribonuclease activities and for understanding the nucleic acid (NA) unwinding-degradation coordination of an exonuclease. Here, using a single-molecule fluorescence resonance energy transfer (smFRET) approach, we show that despite stable binding to both substrates, EXD2 barely cleaves dsDNA and yet displays both exoribonuclease and exodeoxyribonuclease activities toward RNA-DNA hybrids with a cleavage preference for RNA. Unexpectedly, EXD2-mediated hybrid cleavage proceeds in a discrete stepwise pattern, wherein a sudden 4-bp duplex unwinding increment and the subsequent dwell constitute a complete hydrolysis cycle. The relatively weak exodeoxyribonuclease activity of EXD2 partially originates from frequent hybrid rewinding. Importantly, kinetic analysis and comparison of the dwell times under varied conditions reveal two rate-limiting steps of hybrid unwinding and nucleotide excision. Overall, our findings help better understand the cellular functions of EXD2, and the cyclic coupling between duplex unwinding and exonucleolytic degradation may be generalizable to other exonucleases.

Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P

Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of intermediates and the conformational changes that occur during binding are poorly understood. Here, we show that pairing between the 5′ leader and 3′RCCA extending the acceptor stem of ptRNA inhibits ES* formation. Cryo-electron microscopy single particle analysis reveals a dynamic enzyme that becomes ordered upon formation of ES* in which extended acceptor stem pairing is unwound. Comparisons of structures with alternative ptRNAs reveals that once unwinding is completed RNase P primarily uses stacking interactions and shape complementarity to accommodate alternative sequences at its cleavage site. Our study reveals active site interactions and conformational changes that drive molecular recognition by RNase P and lays the foundation for understanding how binding interactions are linked to helix unwinding and catalysis.

Ribonuclease P efficiently processes all tRNA precursors despite sequence variation at the site of cleavage. Here, authors use high-throughput enzymology and cryoEM to reveal conformational changes that drive recognition by bacterial RNase P.

A metal ion-dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase

The metal-dependent M17 aminopeptidases are conserved throughout all kingdoms of life. This large enzyme family is characterized by a conserved binuclear metal center and a distinctive homohexameric arrangement. Recently, we showed that hexamer formation in Plasmodium M17 aminopeptidases was controlled by the metal ion environment, although the functional necessity for hexamer formation is still unclear. To further understand the mechanistic role of the hexameric assembly, here we undertook an investigation of the structure and dynamics of the M17 aminopeptidase from Plasmodium falciparum, PfA-M17. We describe a novel structure of PfA-M17, which shows that the active sites of each trimer are linked by a dynamic loop, and loop movement is coupled with a drastic rearrangement of the binuclear metal center and substrate-binding pocket, rendering the protein inactive. Molecular dynamics simulations and biochemical analyses of PfA-M17 variants demonstrated that this rearrangement is inherent to PfA-M17, and that the transition between the active and inactive states is metal dependent and part of a dynamic regulatory mechanism. Key to the mechanism is a remodeling of the binuclear metal center, which occurs in response to a signal from the neighboring active site and serves to moderate the rate of proteolysis under different environmental conditions. In conclusion, this work identifies a precise mechanism by which oligomerization contributes to PfA-M17 function. Furthermore, it describes a novel role for metal cofactors in the regulation of enzymes, with implications for the wide range of metalloenzymes that operate via a two-metal ion catalytic center, including DNA processing enzymes and metalloproteases.

RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids

RNase H is involved in fundamental cellular processes and is responsible for removing the short stretch of RNA from Okazaki fragments and the long stretch of RNA from R-loops. Defects in RNase H lead to embryo lethality in mice and Aicardi-Goutieres syndrome in humans, suggesting the importance of RNase H. To date, RNase H is known to be a non-sequence-specific endonuclease, but it is not known whether it performs other functions on the structural variants of RNA:DNA hybrids. Here, we used Escherichia coli RNase H as a model, and examined its catalytic mechanism and its substrate recognition modes, using single-molecule FRET. We discovered that RNase H acts as a processive exoribonuclease on the 3' DNA overhang side but as a distributive non-sequence-specific endonuclease on the 5' DNA overhang side of RNA:DNA hybrids or on blunt-ended hybrids. The high affinity of previously unidentified double-stranded (ds) and single-stranded (ss) DNA junctions flanking RNA:DNA hybrids may help RNase H find the hybrid substrates in long genomic DNA. Our study provides new insights into the multifunctionality of RNase H, elucidating unprecedented roles of junctions and ssDNA overhang on RNA:DNA hybrids.

Exploring the dynamic nature of divalent metal ions involved in DNA cleavage by CRISPR-Cas12a

CRISPR-Cas12a has been widely used in genome editing and nucleic acid detection. In both of these applications, Cas12a cleaves target DNA in a divalent metal ion-dependent manner. However, when and how metal ions contribute to the cleavage reaction is unclear. Here, using a single-molecule FRET assay, we reveal that these metal ions are necessary for stabilising cleavage-competent conformations and that they are easily exchangeable, suggesting that they are dynamically coordinated.

Programmable One-Pot Enzymatic Reaction for Direct Fluorescence Detection of Ultralow-Abundance Mutations in the DNA Duplex

Sensitive detection of low-abundance driver mutations may provide valuable information for precise clinical treatment. Compared to next-generation sequencing and droplet digital PCR methods, fluorescent probes show great flexibility in rapid detection of specific mutations with high sensitivity and easily accessible instruments. However, existing approaches with fluorescent probes need an additional step to convert duplex DNA to single-stranded DNA (ssDNA) before the detection step, which increases the time, cost, and risk of loss of low-input target strands. In this work, we attempt to integrate the ssDNA-generation step with the subsequent detection into a programable one-pot reaction by employing lambda exonuclease (λ exo), a versatile nanopore nuclease which exercises different functions on different substrates. The capability of λ exo in discrimination of mismatched bases in 5'- FAM-ended 2 nt-unpaired DNA duplexes was first demonstrated. Specific fluorescent probes were developed for EGFR exon 19 E746-A750del and PIK3CA E545K mutations with discrimination factors as high as 8470 and 884, respectively. By mixing the probes and λ exo with the PCR products of cell-free circulating DNA extracted from plasma samples, the reaction was immediately initiated, which allowed sensitive detection of the two types of mutations at an abundance as low as 0.01% within less than 2 h. Compared to existing approaches, the new method has distinct advantages in simplicity, low cost, and rapidity. It provides a convenient tool for companion diagnostic tests and other routine analysis targeting genetic mutations in clinical samples.

From secretion in Pichia pastoris to application in apple juice processing: Exo-polygalacturonase from Sporothrix schenckii 1099-18

BACKGROUND

Polygalacturonases are a group of enzymes under pectinolytic enzymes related to enzymes that hydrolyse pectic substances. Polygalacturonases have been used in various industrial applications such as fruit juice clarification, retting of plant fibers, wastewater treatment drinks fermentation, and oil extraction.

OBJECTIVES

The study was evaluated at the heterologous expression, purification, biochemical characterization, computational modeling, and performance in apple juice clarification of a new exo-polygalacturonase from Sporothrix schenckii 1099-18 (SsExo-PG) in Pichia pastoris.

METHODS

Recombinant DNA technology was used in this study. Two different pPIC9K plasmids were constructed with native signal sequence-ssexo-pg and alpha signal sequence-ssexo-pg separately. Protein expression and purification performed after plasmids transformed into the Pichia pastoris. Biochemical and structural analyses were performed by using pure SsExo-PG.

RESULTS

The purification of SsExo-PG was achieved using a Ni-NTA chromatography system. The enzyme was found to have a molecular mass of approximately 52 kDa. SsExo-PG presented as stable at a wide range of temperature and pH values, and to be more storage stable than other commercial pectinolytic enzyme mixtures. Structural analysis revealed that the catalytic residues of SsExo-PG are somewhat similar to other Exo-PGs. The KM and kcat values for the degradation of polygalacturonic acid (PGA) by the purified enzyme were found to be 0.5868 µM and 179 s-1, respectively. Cu2+ was found to enhance SsExo-PG activity while Ag2+ and Fe2+ almost completely inhibited enzyme activity. The enzyme reduced turbidity up to 80% thus enhanced the clarification of apple juice. SsExo-PG showed promising performance when compared with other commercial pectinolytic enzyme mixtures.

CONCLUSION

The clarification potential of SsExo-PG was revealed by comparing it with commercial pectinolytic enzymes. The following parameters of the process of apple juice clarification processes showed that SsExo-PG is highly stable and has a novel performance.

Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5' Structure-Specific Nucleases

Enzymes of the 5′ structure-specific nuclease family are crucial for DNA repair, replication, and recombination. One such enzyme is the human exonuclease 1 (hExo1) metalloenzyme, which cleaves DNA strands, acting primarily as a processive 5′-3′ exonuclease and secondarily as a 5′-flap endonuclease. Recently, in crystallo reaction intermediates have elucidated how hExo1 exerts hydrolysis of DNA phosphodiester bonds. These hExo1 structures show a third metal ion intermittently bound close to the two-metal-ion active site, to which recessed ends or 5′-flap substrates bind. Evidence of this third ion has been observed in several nucleic-acid-processing metalloenzymes. However, there is still debate over what triggers the (un)binding of this transient third ion during catalysis and whether this ion has a catalytic function. Using extended molecular dynamics and enhanced sampling free-energy simulations, we observed that the carboxyl side chain of Glu89 (located along the arch motif in hExo1) flips frequently from the reactant state to the product state. The conformational flipping of Glu89 allows one metal ion to be recruited from the bulk and promptly positioned near the catalytic center. This is in line with the structural evidence. Additionally, our simulations show that the third metal ion assists the departure, through the mobile arch, of the nucleotide monophosphate product from the catalytic site. Structural comparisons of nuclease enzymes suggest that this Glu(Asp)-mediated mechanism for third ion recruitment and nucleic acid hydrolysis may be shared by other 5′ structure-specific nucleases.

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12-6 Lennard-Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges. The electronic continuum correction (ECC) can fix this problem through a simple inclusion of solvent polarization effects via ionic charge rescaling. In this work, the development of novel nonbonded models for mono, divalent, and highly charged metal ions is presented. For each metal species, the ionic charge has been scaled, according to the ECC. Lennard-Jones parameters have been optimized using experimental structural and thermodynamic properties as target quantities. Performances of the proposed models are discussed and compared with the literature data, while transferability attitudes among different and well-known water models are evaluated. © 2019 Wiley Periodicals, Inc.

Structure and mechanism of the Red recombination system of bacteriophage λ

While much of this volume focuses on mammalian DNA repair systems that are directly involved in genome stability and cancer, it is important to still be mindful of model systems from prokaryotes. Herein we review the Red recombination system of bacteriophage λ, which consists of an exonuclease for resecting dsDNA ends, and a single-strand annealing protein (SSAP) for binding the resulting 3'-overhang and annealing it to a complementary strand. The genetics and biochemistry of Red have been studied for over 50 years, in work that has laid much of the foundation for understanding DNA recombination in higher eukaryotes. In fact, the Red exonuclease (λ exo) is homologous to Dna2, a nuclease involved in DNA end-resection in eukaryotes, and the Red annealing protein (Redβ) is homologous to Rad52, the primary SSAP in eukaryotes. While eukaryotic recombination involves an elaborate network of proteins that is still being unraveled, the phage systems are comparatively simple and streamlined, yet still encompass the fundamental features of recombination, namely DNA end-resection, homologous pairing (annealing), and a coupling between them. Moreover, the Red system has been exploited in powerful methods for bacterial genome engineering that are important for functional genomics and systems biology. However, several mechanistic aspects of Red, particularly the action of the annealing protein, remain poorly understood. This review will focus on the proteins of the Red recombination system, with particular attention to structural and mechanistic aspects, and how the lessons learned can be applied to eukaryotic systems.