Anti-CRISPR Protein AcrIIC5 Inhibits CRISPR-Cas9 by Occupying the Target DNA Binding Pocket

Anti-CRISPR proteins inhibit CRISPR-Cas immune systems through diverse mechanisms. Previously, the anti-CRISPR protein AcrIIC5_Smu was shown to potently inhibit a type II-C Cas9 from Neisseria meningitidis (Nme1Cas9). In this work, we explore the mechanism of activity of the AcrIIC5 homologue from Neisseria chenwenguii (AcrIIC5_Nch) and show that it prevents Cas9 binding to target DNA. We show that AcrIIC5_Nch targets the PAM-interacting domain (PID) of Nme1Cas9 for inhibition, agreeing with previous findings for AcrIIC5_Smu, and newly establish that strong binding of the anti-CRISPR requires guide RNA be pre-loaded on Cas9. We determined the crystal structure of AcrIIC5_Nch using X-ray crystallography and identified amino acid residues that are critical for its function. Using a protein docking algorithm we show that AcrIIC5_Nch likely occupies the Cas9 DNA binding pocket, thereby inhibiting target DNA binding through a mechanism similar to that previously described for AcrIIA2 and AcrIIA4.     

Substrate specificity of acyl-lipid Δ9-desaturase from <Emphasis Type="Italic">Prochlorothrix hollandica</Emphasis> cyanobacterium producing myristoleic acid

Chlorophyll b-containing cyanobacterium Prochlorothrix hollandica is characterized by a high content of esterified fatty acids (FA) with 14 and 16 carbon atoms in the membrane lipids. Depending on the conditions of cultivation, the relative amount of myristic (C_14:0) and myristoleic (C_14:1) acids can reach 35%, and palmitic (С_16:0) and palmitoleic (С_16:1) acids can reach 60% of the sum of all fatty acids in cells. Monounsaturated FAs are represented by C_14:1, and C_16:1 with an olefinic bond presumably located in the Δ⁹ position. We cloned the gene of acyl-lipid Δ9-desaturase, desC1, from Prochlorothrix hollandica and characterized its specificity to the length of the substrate using the heterologous expression in Escherichia coli cells adding C_14:0 or stearic (C_18:0) acids as exogenous substrates. The results show that DesC1 Δ⁹ desaturase generates olefinic bonds in the FAs with a length of 14 to 18 carbon atoms with an approximately equal efficiency. This indicates that the length of the FA chain in P. hollandica is determined by the activity of the FA synthase, and the chain is desaturated at the Δ⁹ position nonspecifically relatively to its length.     

Hydration Potential of Lysozyme: Protein Dehydration Using a Single Microparticle Technique

For biological molecules in aqueous solution, the hydration pressure as a function of distance from the molecular surface represents a very short-range repulsive pressure that limits atom-atom contact, opposing the attractive van der Waals pressure. Whereas the separation distance for molecules that easily arrange into ordered arrays (e.g., lipids, DNA, collagen fibers) can be determined from x-ray diffraction, many globular proteins are not as easily structured. Using a new micropipette technique, spherical, glassified protein microbeads can be made that allow determination of protein hydration as a function of the water activity (a_w) in a surrounding medium (decanol). By adjusting a_w of the dehydration medium, the final protein concentration of the solid microbead is controlled, and ranges from 700 to 1150 mg/mL. By controlling a_w (and thus the osmotic pressure) around lysozyme, the repulsive pressure was determined as a function of distance between each globular, ellipsoid protein. For separation distances, d, between 2.5 and 9 Å, the repulsive decay length was 1.7 Å and the pressure extrapolated to d = 0 was 2.2 × 10⁸ N/m², indicating that the hydration pressure for lysozyme is similar to other biological interfaces such as phospholipid bilayers.     

A structure-function correlation for fatty acids inSaccharomyces cerevisiae

A relationship which distinguishes those fatty acids that support the growth of oxygen-deprivedSaccharomyces cerevisiae from those that do not was found. To function properly, a long chain of saturated carbon atoms appears to require interruption by an appropriate chemical group such that only a maximum number of contiguous saturated carbon atoms is present anywhere in the chain. A double bond was found to serve as an interrupting group, and for 19cis-unsaturates studied, ranging from C _14:1-Δ⁹ to C_22:6-Δ^{4,7,10,13,16,19}, the number of saturated C atoms was 9. The chain length and the position and number of double bonds had no influence in determining whether the acids were active or inactive except as these structural features related to the interruption rule. Although less extensively examined, a hydroxyl group ortrans-double bond also appeared to act as an interrupting group with allowed numbers of 9 and 7, respectively, for saturated C atoms. Oxygen deprivation did not result in a shift to shorter chain length of the saturates formed, and the presence of unsaturates did not prevent biosynthesis of saturates.     

Posttranslational Modifications of the Histone 3 Tail and Their Impact on the Activity of Histone Lysine Demethylases In Vitro

Posttranslational modifications (PTMs) of the histone H3 tail such as methylation, acetylation and phosphorylation play important roles in epigenetic signaling. Here we study the effect of some of these PTMs on the demethylation rates of methylated lysine 9 in vitro using peptide substrates mimicking histone H3. Various combinations with other PTMs were employed to study possible cross-talk effects by comparing enzyme kinetic characteristics. We compared the kinetics of histone tail substrates for truncated histone lysine demethylases KDM4A and KDM4C containing only the catalytic core (cc) and some combinations were characterized on full length (FL) KDM4A and KDM4C. We found that the substrates combining trimethylated K4 and K9 resulted in a significant increase in the catalytic activity for FL-KDM4A. For the truncated versions of KDM4A and KDM4C a two-fold increase in the catalytic activity toward bis-trimethylated substrates could be observed. Furthermore, a significant difference in the catalytic activity between dimethylated and trimethylated substrates was found for full length demethylases in line with what has been reported previously for truncated demethylases. Histone peptide substrates phosphorylated at T11 could not be demethylated by neither truncated nor full length KDM4A and KDM4C, suggesting that phosphorylation of threonine 11 prevents demethylation of the H3K9me3 mark on the same peptide. Acetylation of K14 was also found to influence demethylation rates significantly. Thus, for truncated KDM4A, acetylation on K14 of the substrate leads to an increase in enzymatic catalytic efficiency (k _cat/K _m), while for truncated KDM4C it induces a decrease, primarily caused by changes in K _m. This study demonstrates that demethylation activities towards trimethylated H3K9 are significantly influenced by other PTMs on the same peptide, and emphasizes the importance of studying these interactions at the peptide level to get a more detailed understanding of the dynamics of epigenetic marks.     

Forced-unfolding and force-quench refolding of RNA hairpins

Nanomanipulation of individual RNA molecules, using laser optical tweezers, has made it possible to infer the major features of their energy landscape. Time-dependent mechanical unfolding trajectories, measured at a constant stretching force (f_S) of simple RNA structures (hairpins and three-helix junctions) sandwiched between RNA/DNA hybrid handles show that they unfold in a reversible all-or-none manner. To provide a molecular interpretation of the experiments we use a general coarse-grained off-lattice Gō-like model, in which each nucleotide is represented using three interaction sites. Using the coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of f_S and the loading rate (r_f). The simulations and theoretical analysis have been done both with and without the handles that are explicitly modeled by semiflexible polymer chains. The mechanisms and timescales for denaturation by temperature jump and mechanical unfolding are vastly different. The directed perturbation of the native state by f_S results in a sequential unfolding of the hairpin starting from their ends, whereas thermal denaturation occurs stochastically. From the dependence of the unfolding rates on r_f and f_S we show that the position of the unfolding transition state is not a constant but moves dramatically as either r_f or f_S is changed. The transition-state movements are interpreted by adopting the Hammond postulate for forced-unfolding. Forced-unfolding simulations of RNA, with handles attached to the two ends, show that the value of the unfolding force increases (especially at high pulling speeds) as the length of the handles increases. The pathways for refolding of RNA from stretched initial conformation, upon quenching f_S to the quench force f_Q, are highly heterogeneous. The refolding times, upon force-quench, are at least an order-of-magnitude greater than those obtained by temperature-quench. The long f_Q-dependent refolding times starting from fully stretched states are analyzed using a model that accounts for the microscopic steps in the rate-limiting step, which involves the trans to gauche transitions of the dihedral angles in the GAAA tetraloop. The simulations with explicit molecular model for the handles show that the dynamics of force-quench refolding is strongly dependent on the interplay of their contour length and persistence length and the RNA persistence length. Using the generality of our results, we also make a number of precise experimentally testable predictions.     

Alternative Exon 9-Encoded Relay Domains Affect More than One Communication Pathway in the Drosophila Myosin Head

We investigated the biochemical and biophysical properties of one of the four alternative regions within the Drosophila myosin catalytic domain: the relay domain encoded by exon 9. This domain of the myosin head transmits conformational changes in the nucleotide-binding pocket to the converter domain, which is crucial to coupling catalytic activity with mechanical movement of the lever arm. To study the function of this region, we used chimeric myosins (IFI-9b and EMB-9a), which were generated by exchange of the exon 9-encoded domains between the native embryonic body wall (EMB) and indirect flight muscle isoforms (IFI). Kinetic measurements show that exchange of the exon 9-encoded region alters the kinetic properties of the myosin S1 head. This is reflected in reduced values for ATP-induced actomyosin dissociation rate constant (K₁k₊₂) and ADP affinity (K_AD), measured for the chimeric constructs IFI-9b and EMB-9a, compared to wild-type IFI and EMB values. Homology models indicate that, in addition to affecting the communication pathway between the nucleotide-binding pocket and the converter domain, exchange of the relay domains between IFI and EMB affects the communication pathway between the nucleotide-binding pocket and the actin-binding site in the lower 50-kDa domain (loop 2). These results suggest an important role of the relay domain in the regulation of actomyosin cross-bridge kinetics.     

Effects of alkyl chain length of gallates on their antifungal property and potency as an environmentally benign preservative against wood-decay fungi

This study investigated effects of alkyl chain length of eight aliphatic gallates from C₁ to C₁₈ on their antifungal activity and free radical scavenging activity, which are two important indicators in developing wood preservatives. Results from the agar plate test showed that the antifungal activity against wood-rot fungi of gallates was related to alkyl chain length. It increased with increasing alkyl chain length, reaching a maximum at octyl gallate (C₈), and then decreased as chain length increased. Octyl gallate also exhibited potential antifungal activity against soft-rot Chaetomium globosum and copper-tolerant fungi Wolfiporia extensa and Poria placenta, which are difficult to combat with current copper-based wood preservatives. Octyl gallate is a potent antifungal agent with excellent antifungal activity over a broad antifungal spectrum. All of the gallates tested, regardless of their alkyl chain length, showed strong scavenging activity on the DPPH radical with EC₅₀ values around 1–5 μg ml^?1, indicating that the alkyl chain length was not directly related to this activity. Results from the soil block test showed that excellent antioxidants such as propyl gallate (C₃) and octyl gallate impart wood with good resistance against wood-decay fungi. This suggests that antioxidants have potential as environmentally benign wood preservatives.     

Glutamylation on alpha-tubulin is not essential but affects the assembly and functions of a subset of microtubules in Tetrahymena thermophila

Tubulin undergoes glutamylation, a conserved posttranslational modification of poorly understood function. We show here that in the ciliate Tetrahymena, most of the microtubule arrays contain glutamylated tubulin. However, the length of the polyglutamyl side chain is spatially regulated, with the longest side chains present on ciliary and basal body microtubules. We focused our efforts on the function of glutamylation on the α-tubulin subunit. By site-directed mutagenesis, we show that all six glutamates of the C-terminal tail domain of α-tubulin that provide potential sites for glutamylation are not essential but are needed for normal rates of cell multiplication and cilium-based functions (phagocytosis and cell motility). By comparative phylogeny and biochemical assays, we identify two conserved tubulin tyrosine ligase (TTL) domain proteins, Ttll1p and Ttll9p, as α-tubulin-preferring glutamyl ligase enzymes. In an in vitro microtubule glutamylation assay, Ttll1p showed a chain-initiating activity while Ttll9p had primarily a chain-elongating activity. GFP-Ttll1p localized mainly to basal bodies, while GFP-Ttll9p localized to cilia. Disruption of the TTLL1 and TTLL9 genes decreased the rates of cell multiplication and phagocytosis. Cells lacking both genes had fewer cortical microtubules and showed defects in the maturation of basal bodies. We conclude that glutamylation on α-tubulin is not essential but is required for efficiency of assembly and function of a subset of microtubule-based organelles. Furthermore, the spatial restriction of modifying enzymes appears to be a major mechanism that drives differential glutamylation at the subcellular level.     

Evidence for Receptor Function of Auxin Binding Sites in Maize : RED LIGHT INHIBITION OF MESOCOTYL ELONGATION AND AUXIN BINDING

When 3- to 4-day-old dark-grown maize (Zea mays L. WF9 × Bear 38) seedlings are given red light, auxin-binding activity localized on endoplasmic reticulum membranes of the mesocotyl begins to decrease after 4 hours; by 9 hours, it falls to 50 to 60% of that in dark controls, on either a fresh weight or total particulate protein basis. Endoplasmic reticulum-localized NADH:cytochrome c reductase activity decreases in parallel. Loss of binding is due to decrease in number of sites, with no change in their affinity for auxin (K_d 0.2 micromolar for naphthalene-1-acetic acid). Elongation of mesocotyl segments in response to auxin decreases with a similar time course. Elongation of segments from irradiated plants shows the same apparent affinity for auxin as that of the dark controls. Auxin-binding activity and elongation response also decrease in parallel down the length of the mesocotyl. These observations are consistent with a role of endoplasmic reticulum-localized auxin binding sites as receptors for auxin action in cell elongation.     

Glutathione-related inhibition of prostaglandin metabolism

Placental homogenates contain a heat-stable, dialyzable fraction which specifically inhibits two placental enzymes, both of which possess 15-hydroxyprostaglandin dehydrogenase and 9-ketoprostaglandin reductase activities. The inhibition of the two enzymes is the same. The inhibitor has been resolved into two components by gel filtration on a column of Sephadex LH-20. The component which eluted first has been identified as oxidized glutathione (GSSG), the other as a glutathione-containing material (GSX). Inhibition of the 15-hydroxyprostaglandin dehydrogenase activity is competitive with respect to the prostaglandin substrate (K_i^GSSG = 26 μM, K_i^GSX = 1.4 μM). Inhibition of the 9-ketoprostaglandin reductase activity is also competitive with respect to the prostaglandin substrate (K_i^GSSG = 68 μM). The most effective inhibitor of the 15-hydroxyprostaglandin dehydrogenase is the prostaglandin A₁-glutathione adduct (K_i = 0.27 μM). This compound is not a substrate for oxidation of the 15-hydroxyl group but it is the best substrate found to date for reduction of the 9-keto function.     

A Phenomenological Theory of Muscular Contraction: II. Generalized Length Variations

In part I of this series, the theory of irreversible thermodynamics was applied to the sliding filament model to obtain rate equations for a contracting muscle at the in situ length l_o. In this paper we extend the theory to include length variations derived from the sliding filament model of contracting muscle using the work of Gordon, Huxley, and Julian (1). Accepting the validity of Hill's forcevelocity relation (2) at the in situ length, we show that Hill's equation is valid for any length provided that the values of the parameters, a, b, and V_m vary with length as derived herein. The predicted variation with length of the velocity for a lightly loaded isotonic contraction is shown to agree well with that measured by Gordon, Huxley, and Julian (1). Chemical rates are derived as functions of length using parameters that can be obtained experimentally.     

Synthesis and cancer cell cytotoxicity of substituted xanthenes

A series of substituted xanthenes was synthesized and screened for activity using DU-145, MCF-7, and HeLa cancer cell growth inhibition assays. The most potent compound, 9g ([N,N-diethyl]-9-hydroxy-9-(3-methoxyphenyl)-9H-xanthene-3-carboxamide), was found to inhibit cancer cell growth with IC₅₀ values ranging from 36 to 50 μM across all three cancer cell lines. Structure–activity relationship (SAR) data is presented that indicates additional gains in potency may be realized through further derivatization of the compounds (e.g., the incorporation of a 7-fluoro substituent to 9g). Results are also presented that suggest the compounds function through a unique mechanism of action as compared to that of related acridine and xanthone anticancer agents (which have been shown to intercalate into DNA and inhibit topoisomerase II activity). A structural comparison of these compounds suggests the differences in function may be due to the structure of the xanthene heterocycle which adopts a nonplanar conformation about the pyran ring.     

Growth Promotion in Pea Stem Sections. III. By Alkyl Nitriles, Alkyl Acetylenes and Insect Juvenile Hormones

C₁₄, C₁₅, and C₁₆ alkyl nitriles, and C₁₆ and C₁₈ alkyl acetylenes at 10 to 105 micromolar concentrations promote the growth of stem sections from red-light-exposed seedlings of dwarf peas (Pisum sativum L. cv. Progress No. 9). Similar results were obtained with substances active as insect juvenile hormones, namely farnesol, the racemic ethyl ester of 1 of the natural hormones, and a “synthetic juvenile hormone” mixture, the latter 2 having as high an activity in the pea assay as any lipid reported previously. A sterically nearly identical compound, methyl-RS-10,11-epoxyfarnesoate, is a weak insect hormone and did not promote plant growth. Thus activity in peas and in insects is in some cases parallel. Other similarities and some differences are discussed. Peas appear to require molecules longer than 20A, while insect activity is maximal at that length. All active molecules are ineffective in promoting pea stem elongation by themselves, indole acetic acid must also be present. The lipid effect in plants and the juvenile hormone response in insects have much in common and the evidence suggests they could have a similar locus of action in a membrane controlling respiratory function.     

Quantitative Transcription Factor Binding Kinetics at the Single-Molecule Level

We investigated the binding interaction between the bacteriophage λ-repressor CI and its target DNA using total internal reflection fluorescence microscopy. Large stepwise changes in the intensity of the red fluorescent protein fused to CI were observed as it associated with and dissociated from individually labeled single-molecule DNA targets. The stochastic association and dissociation were characterized by Poisson statistics. Dark and bright intervals were measured for thousands of individual events. The exponential distribution of the intervals allowed direct determination of the association and dissociation rate constants (k_a and k_d, respectively). We resolved in detail how k_a and k_d varied as a function of three control parameters: the DNA length L, the CI dimer concentration, and the binding affinity. Our results show that although interactions with nonoperator DNA sequences are observable, CI binding to the operator site is not dependent on the length of flanking nonoperator DNA.     

Molecular weight and pH aspects of the efficacy of oligochitosan against methicillin-resistant Staphylococcus aureus (MRSA)

Oligochitosan samples varying in molecular weight (M_w) and having narrow polydispersities were prepared by means of depolymerization of chitosan in hydrochloric acid, and their antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) was measured at pH values 5.5-8.0. The antibacterial testing of oligochitosans obtained showed that oligochitosans having M_w in the range of 0.73-20.0 kDa could be used both at slightly acidic and neutral pH values, and that the activity against MRSA remained moderate for oligochitosan samples having M_w about 3-5 kDa even at slightly basic pH values. The self-assembling behavior of oligochitosan macromolecules in the dilute solution at various pH values as a function of chain length was investigated. At first it was shown that oligochitosans formed supramolecular aggregates in dilute solutions below the critical pH value 6.5. Despite the aggregation phenomenon, the formation of nano-sized aggregates did not prevent oligochitosan from demonstrating the bactiostatic activity.     

Amino acid positions 69-132 of UGT1A9 are involved in the C-glucuronidation of phenylbutazone

Phenylbutazone (PB) is known to be biotransformed to its O- and C-glucuronide. Recently, we reported that PB C-glucuronide formation is catalyzed by UGT1A9. Interestingly, despite UGT1A8 sharing high amino acid sequence identity with UGT1A9, UGT1A8 had no PB C-glucuronidating activity. In the present study, we constructed eight UGT1A9/UGT1A8 chimeras and evaluated which region is important for PB C-glucuronide formation. All of the chimeras and UGT1A8 and UGT1A9 had 7-hydroxy-(4-trifluoromethyl)coumarin (HFC) O-glucuronidating activity. The K_m values for HFC glucuronidation of UGT1A8, UGT1A9 and their chimeras were divided into two types, UGT1A8 type (high K_m) and UGT1A9 type (low K_m), and these types were determined according to whether their amino acids at positions 69-132 were those of UGT1A8 or UGT1A9. Likewise, PB O-glucuronidating activity was also detected by all of the chimeras, and their K_m values were divided into two types. On the contrary, PB C-glucuronidating activity was detected by UGT1A9_(1-132)/1A8_(133-286), UGT1A9_(1-212)/1A8_(213-286), UGT1A8_(1-68)/1A9_(69-286), and UGT1A8_(1-68)/1A9_(69-132)/1A8_(133-286) chimeras. The region 1A9_(69-132) was common among chimeras having PB C-glucuronidating activity. Of interest is that UGT1A9_(1-68)/1A8_(69-132)/1A9_(133-286) had lost PB C-glucuronidation activity, but retained activities of PB and HFC O-glucuronidation. These results strongly suggested that amino acid positions 69-132 of UGT1A9 are responsible for chemoselectivity for PB and affinity to substrates such as PB and HFC.