Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis

Radical S-adenosyl-l-methionine (SAM) enzymes comprise a vast superfamily catalyzing diverse reactions essential to all life through homolytic SAM cleavage to liberate the highly reactive 5'-deoxyadenosyl radical (5'-dAdo·). Our recent observation of a catalytically competent organometallic intermediate Ω that forms during reaction of the radical SAM (RS) enzyme pyruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an intermediate under a variety of mixing order conditions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double resonance spectroscopy establish that Ω involves an Fe-C5' bond between 5'-dAdo· and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (coenzyme B₁₂) cofactor used to initiate radical reactions via a 5'-dAdo· intermediate. Liberation of a reactive 5'-dAdo· intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B₁₂. However, coenzyme B₁₂ is involved in enzymes catalyzing only a small number (∼12) of distinct reactions, whereas the RS superfamily has more than 100 000 distinct sequences and over 80 reaction types characterized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.

Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis

Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.

A structurally-characterized peroxomanganese(iv) porphyrin from reversible O2 binding within a metal-organic framework

Within a MOF, a side-on peroxomanganese(iv) porphyrin has been isolated and comprehensively examined.

The role of peroxometal species as reactive intermediates in myriad biological processes has motivated the synthesis and study of analogous molecular model complexes. Peroxomanganese(iv) porphyrin complexes are of particular interest, owing to their potential ability to form from reversible O₂ binding, yet have been exceedingly difficult to isolate and characterize in molecular form. Alternatively, immobilization of metalloporphyrin sites within a metal–organic framework (MOF) can enable the study of interactions between low-coordinate metal centers and gaseous substrates, without interference from bimolecular reactions and axial ligation by solvent molecules. Here, we employ this approach to isolate the first rigorously four-coordinate manganese(ii) porphyrin complex and examine its reactivity with O₂ using infrared spectroscopy, single-crystal X-ray diffraction, EPR spectroscopy, and O₂ adsorption analysis. X-ray diffraction experiments reveal for the first time a peroxomanganese(iv) porphyrin species, which exhibits a side-on, η² binding mode. Infrared and EPR spectroscopic data confirm the formulation of a peroxomanganese(iv) electronic structure, and show that O₂ binding is reversible at ambient temperature, in contrast to what has been observed in molecular form. Finally, O₂ gas adsorption measurements are employed to quantify the enthalpy of O₂ binding as h_ads = –49.6(8) kJ mol^–1. This enthalpy is considerably higher than in the corresponding Fe- and Co-based MOFs, and is found to increase with increasing reductive capacity of the M^II/III redox couple.

Isolation and characterization of a high-spin mixed-valent iron dinitrogen complex

We report a rare example of a mixed-valence iron compound with an FeNNFe core, which gives insight into the structural, spectroscopic, and magnetic influences of single-electron reductions and oxidations. In the new compound, the odd electron is localized as judged from Mössbauer spectra at 80 K and infrared spectra at room temperature, and the backbonding into the N2 unit is intermediate between diiron(i) and diiron(0) congeners. Magnetic susceptibility and relaxation studies on the series of FeNNFe compounds show significant magnetic anisotropy, but through-barrier pathways enable fairly rapid magnetic relaxation.

The bridge helix of Cas12a imparts selectivity in cis-DNA cleavage and regulates trans-DNA cleavage

Cas12a is an RNA-guided DNA endonuclease of the type V-A CRISPR-Cas system that has evolved convergently with the type II Cas9 protein. We previously showed that proline substitutions in the bridge helix (BH) impart target DNA cleavage selectivity in Streptococcus pyogenes (Spy) Cas9. Here, we examined a BH variant of Cas12a from Francisella novicida (FnoCas12aKD2P ) to test mechanistic conservation. Our results show that for RNA-guided DNA cleavage (cis-activity), FnoCas12aKD2P accumulates nicked products while cleaving supercoiled DNA substrates with mismatches, with certain mismatch positions being more detrimental for linearization. FnoCas12aKD2P also possess reduced trans-single-stranded DNA cleavage activity. These results implicate the BH in substrate selectivity in both cis- and trans-cleavages and show its conserved role in target discrimination among Cas nucleases.

CRISPR-Cas12a Nucleases Bind Flexible DNA Duplexes without RNA/DNA Complementarity

Cas12a (also known as "Cpf1") is a class 2 type V-A CRISPR-associated nuclease that can cleave double-stranded DNA at specific sites. The Cas12a effector enzyme comprises a single protein and a CRISPR-encoded small RNA (crRNA) and has been used for genome editing and manipulation. Work reported here examined in vitro interactions between the Cas12a effector enzyme and DNA duplexes with varying states of base-pairing between the two strands. The data revealed that in the absence of complementarity between the crRNA guide and the DNA target-strand, Cas12a binds duplexes with unpaired segments. These off-target duplexes were bound at the Cas12a site responsible for RNA-guided double-stranded DNA binding but were not cleaved due to the lack of RNA/DNA hybrid formation. Such promiscuous binding was attributed to increased DNA flexibility induced by the unpaired segment present next to the protospacer-adjacent-motif. The results suggest that target discrimination of Cas12a can be influenced by flexibility of the DNA. As such, in addition to the linear sequence, flexibility and other physical properties of the DNA should be considered in Cas12a-based genome engineering applications.

Coordinated Actions of Cas9 HNH and RuvC Nuclease Domains Are Regulated by the Bridge Helix and the Target DNA Sequence

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.

Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions

Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date.

Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date. We here demonstrate an efficient and generally applicable posttranscriptional SDSL method for large RNAs using an expanded genetic alphabet containing the NaM-TPT3 unnatural base pair (UBP). An alkyne-modified TPT3 ribonucleotide triphosphate (rTPT3^COTP) is synthesized and site-specifically incorporated into large RNAs by in vitro transcription, which allows attachment of the azide-containing nitroxide through click chemistry. We validate this strategy by SDSL of a 419-nucleotide ribonuclease P (RNase P) RNA from Bacillus stearothermophilus under non-denaturing conditions. The effects of site-directed UBP incorporation and subsequent spin labeling on the global structure and function of RNase P are marginal as evaluated by Circular Dichroism spectroscopy, Small Angle X-ray Scattering, Sedimentation Velocity Analytical Ultracentrifugation and enzymatic assay. Continuous-Wave EPR analyses reveal that the labeling reaction is efficient and specific, and Pulsed Electron–Electron Double Resonance measurements yield an inter-spin distance distribution that agrees with the crystal structure. The labeling strategy as presented overcomes the size constraint of RNA labeling, opening new avenues of spin labeling and EPR spectroscopy for investigating the structure and dynamics of large RNAs.

Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes

Measurement of distances between spectroscopic labels (e.g., spin labels, fluorophores) attached to specific sites of biomolecules is an important method for studying biomolecular complexes. ALLNOX (Addition of Labels and Linkers) has been developed as a program to model interlabel distances based on an input macromolecule structure. Here, we report validation of ALLNOX using measured distances between nitroxide spin labels attached to specific sites of a protein-DNA complex. The results demonstrate that ALLNOX predicts average interspin distances that matched with values measured with pairs of labels attached at the protein and/or DNA. This establishes a solid foundation for using spin labeling in conjunction with ALLNOX to investigate complexes without high-resolution structures. With its high degree of flexibility for the label or the target biomolecule, ALLNOX provides a useful tool for investigating the structure-function relationship in a large variety of biological molecules.

Efficient Detection Using Soft Computing Approach of Modified Fuzzy C-Means Based Outlier Detection in Electronics Patient Records Systems

Outliers are the data objects or data elements which are deviated from the observation or population in the dataset. Normally outliers are considered as noise data but in recent days outliers are taken vital role in the applications like healthcare systems to energetically check for any malignant, irregular, or abnormal behaviour. Accuracy of the outlier detection is purely based upon the efficiency of outlier detection methods and application where the outlier detection is involved. In this paper we design hybrid three phase modified fuzzy c-means and diverse distance based outlier detection method for distributed dataset to detect the unusual usage of data and illegitimate approach in large-scale integral networks, especially in healthcare sectors (EPR systems). The proposed algorithm combining the features of modified C-Means Fuzzification, Z-score and Manhattan distance in outlier identification. The proposed algorithm provides efficiency in outlier detection on univariate EPRdata. This paper also mainly focuses the application intrusion detection in healthcare data. The algorithm is tested on real world dataset of machine learning database repository (UCIML).

Prophylactically Feeding Manganese to Drosophila Confers Sex-Specific Protection from Acute Ionizing Radiation Independent of MnSOD2 Levels

Ionizing radiation is a health threat to many, including warfighters, radiological emergency responders, radiotherapy patients, and astronauts. Despite this, no FDA-approved prophylactic medical countermeasures exist to attenuate the symptoms that occur from radiation exposure. Manganese has recently been shown to be critical for radioresistance in a wide range of organisms. In this study, we designed a stringent feeding method to test the prophylactic effects of dietary manganese on Drosophila's lifespan before exposure to acute irradiation. We found that male flies have substantially lower radioresistance than females, but feeding with low doses of MnCl2 before acute irradiation exposure extends male survival to that of females. Whole animal electron paramagnetic resonance analyses showed males have lower amounts of high-symmetry manganese-metabolite antioxidant complexes (H-Mn) than females, but manganese supplementation increases H-Mn to female levels. Levels of mitochondrial free-radical scavenger manganese-superoxide-dismutase 2 (MnSOD2) did not increase after acute irradiation, nor did loss of MnSOD2 sensitize larvae to acute irradiation exposure. These data support that prophylactic manganese feeding is sufficient to increase survivorship in males subjected to acute irradiation, independent of MnSOD2 levels, indicating a role of antioxidant manganese-metabolite H-Mn complexes for radioprotection. Furthermore, this Drosophila feeding method could be used to identify additional radiation countermeasures.

Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome

DNA methylation at cytosine bases (5-methylcytosine, 5mC) is a heritable epigenetic mark regulating gene expression. While enzymes that metabolize 5mC are well-characterized, endogenous signaling molecules that regulate DNA methylation machinery have not been described. We report that physiological nitric oxide (NO) concentrations reversibly inhibit the DNA demethylases TET and ALKBH2 by binding to the mononuclear non-heme iron atom forming a dinitrosyliron complex (DNIC) and preventing cosubstrates from binding. In cancer cells treated with exogenous NO, or endogenously synthesizing NO, 5mC and 5-hydroxymethylcytosine (5hmC) increase, with no changes in DNA methyltransferase activity. 5mC is also significantly increased in NO-producing patient-derived xenograft tumors from mice. Genome-wide methylome analysis of cells chronically treated with NO (10 days) shows enrichment of 5mC and 5hmC at gene-regulatory loci, correlating with altered expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO signaling and represents a unique epigenetic role for NO.