Precise A•T to G•C base editing in the zebrafish genome

Background

Base editors are a class of genome editing tools with the ability to efficiently induce point mutations in genomic DNA, without inducing double-strand breaks or relying on homology-direct repair as in other such technologies. Recently, adenine base editors (ABEs) have been developed to mediate the conversion of A?T to G?C in genomic DNA of human cells, mice, and plants. Here, we investigated the activity and efficiency of several adenine base editors in zebrafish and showed that base editing can be used to create new models of pathogenic diseases caused by point mutations.

Results

The original ABE7.10 exhibits almost no activity in zebrafish. After codon optimization, we found that a zABE7.10 variant could induce targeted conversion of adenine to guanine in zebrafish at multiple tested genomic loci, and all the target sites showed a high rate of germline targeting efficiency. Furthermore, using this system, we established a zebrafish model of 5q-Syndrome that contained a new point mutation in rps14. The further modification of zABE7.10 by a bipartite nuclear localization signals (bpNLS) resulted in 1.96-fold average improvement in ABE-mediated editing efficiency at four sites.

Conclusions

Collectively, this system, designated as zABE7.10, provides a strategy to perform A?T to G?C base editing in zebrafish and enhances its capacity to model human diseases.

     

"绿色革命"之父诺曼•博洛格

在第一次"绿色革命"中,国际玉米小麦改良中心做出了突出的贡献,而在这个国际组织中,小麦项目的创始人和领导者是大名鼎鼎的美国小麦育种专家诺曼?博洛格(Norman Borlaug). 诺曼?博洛格于1914年出生在美国艾奥瓦州,是美国著名的农业科学家、植物病理学家、遗传育种学家.他于1944年到达墨西哥从事农业科学研究,...     

Reaction of peroxynitrite with carbon dioxide: intermediates and determination of the yield of CO3 •– and NO2 •

CO2 catalyses the isomerization of the biological toxin ONOO- to NO3- via an intermediate, presumably ONOOCO2-, which has an absorption maximum near 650 nm. The reflection spectrum of solid NMe4+ ONOO- exposed to CO2 shows a similar band near 650 nm; this absorption decays over minutes. Stopped-flow experiments in which CO2 solutions were mixed with alkaline ONOO- solutions indicate the formation of at least one intermediate. The initial absorption at 302 nm is less than that of ONOO-, which indicates that reactions take place within the mixing time, and this absorption is dependent (but not linearly) on the ONOO- and CO2 concentrations. We found that reaction of peroxynitrite with carbon dioxide forms some trioxocarbonate(*1-) (CO3*-) and nitrogen dioxide (NO2*) radicals via homolysis of the O-O bond in ONOOCO2-. We determined the extent of radical formation by mixing peroxynitrite, carbon dioxide and nitrogen monoxide. The later reacts with CO3*- and NO2* radicals to form, effectively, three NO2- per homolysis; ONOOCO2- that does not undergo homolysis yields NO3- and CO2. Based on the NO3- and NO2- analyses, the extent of conversion to NO3- is 96 +/- 1% and that of homolysis is 3 +/- 1%, respectively, significantly less than that reported in the literature.     

Stimulation and oxidative catalytic inactivation of thermolysin by copper•Cys-Gly-His-Lys

[Cu²⁺•Cys-Gly-His-Lys] stimulates thermolysin (TLN) activity at low concentration (below 10 μM) and inhibits the enzyme at higher concentration, with binding affinities of 2.0 and 4.9 μM, respectively. The metal-free Cys-Gly-His-Lys peptide also stimulates TLN activity, with an apparent binding affinity of 2.2 μM. Coordination of copper through deprotonated imine nitrogens, the histidyl nitrogen, and the free N-terminal amino group is consistent with the characteristic absorption spectrum of a Cu²⁺–amino-terminal copper and nickel binding motif (λ _max ∼ 525 nm). The lack of thiol coordination is suggested by both the absence of a thiol to Cu²⁺ charge transfer band and electrochemical studies, since the electrode potential (vs. Ag/AgCl) 0.84 V (ΔE = 92 mV) for the Cu^3+/2+ redox couple obtained for [Cu²⁺•Cys-Gly-His-Lys] was found to be in close agreement with that of a related complex [Cu²⁺•Lys-Gly-His-Lys]⁺ (0.84 V, ΔE = 114 mV). The N-terminal cysteine appears to be available as a zinc-anchoring residue and plays a critical functional role since the [Cu²⁺•Lys-Gly-His-Lys]⁺ homologue exhibits neither stimulation nor inhibition of TLN. Under oxidizing conditions (ascorbate/O₂) the catalyst is shown to mediate the complete irreversible inactivation of TLN at concentrations where enzyme activity would otherwise be stimulated. The observed rate constant for inactivation of TLN activity was determined as k _obs = 7.7 × 10⁻² min⁻¹, yielding a second-order rate constant of (7.7 ± 0.9) × 10⁴ M⁻¹ min⁻¹. Copper peptide mediated generation of reactive oxygen species that subsequently modify active-site residues is the most likely pathway for inactivation of TLN rather than cleavage of the peptide backbone.     

Semiquinone-iron complex of photosystem II: EPR signals assigned to the low-field edge of the ground state doublet of QA•-Fe2+ and QB•-Fe2+

The quinone-iron complex of the electron acceptor complex of Photosystem II was studied by EPR spectroscopy in Thermosynechococcus elongatus. New g ～ 2 features belonging to the EPR signal of the semiquinone forms of the primary and secondary quinone, i.e., Q(A)(?-)Fe(2+) and Q(B)(?-)Fe(2+), respectively, are reported. In previous studies, these signals were missed because they were obscured by the EPR signal arising from the stable tyrosyl radical, TyrD(?). When the TyrD(?) signal was removed, either by chemical reduction or by the use of a mutant lacking TyrD, the new signals dominated the spectrum. For Q(A)(?-)Fe(2+), the signal was formed by illumination at 77 K or by sodium dithionite reduction in the dark. For Q(B)(?-)Fe(2+), the signal showed the characteristic period-of-two variations in its intensity when generated by a series of laser flashes. The new features showed relaxation characteristics comparable to those of the well-known features of the semiquinone-iron complexes and showed a temperature dependence consistent with an assignment to the low-field edge of the ground state doublet of the spin system. Spectral simulations are consistent with this assignment and with the current model of the spin system. The signal was also present in Q(B)(?-)Fe(2+) in plant Photosystem II, but in plants, the signal was not detected in the Q(A)(?-)Fe(2+) state.     

A Neutron Scattering Study of the Ternary Complex EF-Tu•GTP-valy1-tRNAVal 1A

Abstract

The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNA^Val _1A has been investigated in a hepes buffer of “pH” 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D₂O where EF-Tu (42% D₂O) and tRNA (71% D₂O) are successively matched by the solvents. The results indicate that EF-Tu undergoes a conformational change and contracts as a result of the complex formation, since the radius of gyration decreases by 15% from 2.82 to 2.39 nm. tRNA^Val _1A, on the other hand, seems to mainly retain its conformation within the complex, since the radii of gyration for the free (after correction for interparticular scattering) and complexed form are essentially the same. 2.38 and 2.47 nm, respectively.     

Effect of •OH scavenging action by non-SH-containing angiotensin converting enzyme inhibitor imidaprilat using microdialysis

We examined the effect of non-SH-containing angiotensin converting enzyme (ACE) inhibitor imidaprilat on hydroxyl radical (•OH) generation using microdialysis. Salicylic acid in Ringer's solution containing sodium salicylate (0.5 n mol μL⁻¹ min⁻¹) was infused directly through a microdialysis probe to detect the generation of •OH as reflected by the formation of 2,3-dihydroxybenzoic acid (DHBA) in the myocardium of anesthetized rats. We compared the ability of two non-SH-containing ACE inhibitors (imidaprilat and enalaprilat) with an -SH-containing ACE inhibitor (captopril) to scavenge the •OH. When iron (II) was administered to animals pretreated with these three ACE inhibitors, a decrease in 2,3-DHBA of all three compounds was observed, as compared with the iron (II) only-treated group. All three ACE inhibitors were able to scavenge •OH generated by the action of iron (II). However, imidaprilat is a free radical scavenger more potent than enalaprilat. These results suggested that ACE inhibitors are probably not only related to the presence of the SH radical.     

Stabilization of G•C-Containing DNA Duplexes by Polyamides with Parallel Orientation in the Minor Groove

The polyamides based on 4-amino-1-methylpyrrol-2-carboxylic acid, 4-amino-1-methylimidazole-2-carboxylic acid, and -alanine that stabilize oligonucleotide duplexes consisting of GC pairs through parallel packing in the minor groove were studied. The initial duplex TTGCGCpGCGCAA melts at 28°C; the TTGCGCp[NH(CH₂)₃COPyImImNH(CH₂)₃NH(CH₃)₂][NH(CH₂)₃COImImPyNH(CH₂)₃N(CH₃)₂]GCGCAA duplex (bisphosphoramidate with parallel orientation of ligands, where Py, Im, and are the residues of 1-methyl-4-aminopyrrol-2-carboxylic and 1-methyl-4-aminoimidazole-2-carboxylic acids and -alanine, respectively), at 48°C; and the TTGCGCp[NH(CH₂)₃COImImPyNH(CH₂)₃COImImPyNH(CH₂)₃N(CH₃)₂]GCGCAA duplex (a hairpin structure with antiparallel orientation), at 56°C.     

Computational modeling of the adsorption and •OH initiated photochemical and photocatalytic primary oxidation of nitrobenzene

The adsorption and primary oxidation step for the photodegradation of nitrobenzene (NB) have been studied computationally using MSINDO SCF MO method. The method performs efficiently for extended surface models such as Ti₃₆O₉₀H₃₆. Molecular dynamics simulations have revealed that NB is linked to TiO₂ surface at the titanium ion via the oxygen atoms of NO₂ group. In addition, the computed vibrational density of states for the adsorbed NB molecule is in reasonably good agreement with the available experimental data and theoretical results. In order to identify the primary photochemical and photocatalytic ^•OH initiated photooxidation intermediates, we have employed two different theoretical approaches, frontier orbital theory and Wheland localization theory. It has been found that the meta- hydroxynitrocyclohexadienyl radical is energetically more favored than para- and ortho-hydroxynitrocyclohexadienyl radicals for the photochemical photolysis, whereas in the case of photocatalysis, the ^•OH radical attack is unselective and all three possible isomers have comparable stabilities. Figure Minimum energy adsorption conformation of nitrobenzene onto TiO₂ (100) surface     

Crystal structure of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase•dihydropteroate synthase bifunctional enzyme from Francisella tularensis

The 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) enzymes catalyze sequential metabolic reactions in the folate biosynthetic pathway of bacteria and lower eukaryotes. Both enzymes represent validated targets for the development of novel anti-microbial therapies. We report herein that the genes which encode FtHPPK and FtDHPS from the biowarfare agent Francisella tularensis are fused into a single polypeptide. The potential of simultaneously targeting both modules with pterin binding inhibitors prompted us to characterize the molecular details of the multifunctional complex. Our high resolution crystallographic analyses reveal the structural organization between FtHPPK and FtDHPS which are tethered together by a short linker. Additional structural analyses of substrate complexes reveal that the active sites of each module are virtually indistinguishable from those of the monofunctional enzymes. The fused bifunctional enzyme therefore represents an excellent vehicle for finding inhibitors that engage the pterin binding pockets of both modules that have entirely different architectures. To demonstrate that this approach has the potential of producing novel two-hit inhibitors of the folate pathway, we identify and structurally characterize a fragment-like molecule that simultaneously engages both active sites. Our study provides a molecular framework to study the enzyme mechanisms of HPPK and DHPS, and to design novel and much needed therapeutic compounds to treat infectious diseases.     

NMR Studies of Triplex Formation - Recognition of C•G Base Pairs by New Heterocyclic Systems

Abstract

Sequence specific recognition of double stranded DNA by oligonucleotides is an important process for selective control of gene expression. However, triple-helix formation is limited to recognition of DNA homopurine strands. We report herein the NMR recognition studies of C?G base pairs by new heterocyclic systems like benzimidazole and benzoxazoles bearing an urea donor function designed to bound to the O4 and N7 atoms of guanosine base.     

The mechanism of (+) taxifolin’s protective antioxidant effect for •OH-treated bone marrow-derived mesenchymal stem cells

The natural dihydroflavonol (+) taxifolin was investigated for its protective effect on Fenton reagent-treated bone marrow-derived mesenchymal stem cells (bmMSCs). Various antioxidant assays were used to determine the possible mechanism. These included ?OH-scavenging, 2-phenyl-4, 4, 5, 5-tetramethylimidazoline-1-oxyl-3-oxide radical-scavenging (PTIO?-scavenging), 1, 1-diphenyl-2-picryl-hydrazl radical-scavenging (DPPH?-scavenging), 2, 2′-azino-bis (3-ethylbenzo-thiazoline-6-sulfonic acid) radical-scavenging (ABTS⁺?-scavenging), Fe³⁺-reducing, and Cu²⁺-reducing assays. The Fe²⁺-binding reaction was also investigated using UV-Vis spectra. The results revealed that cell viability was fully restored, even increasing to 142.9?±?9.3% after treatment with (+) taxifolin. In the antioxidant assays, (+) taxifolin was observed to efficiently scavenge ?OH, DPPH? and ABTS⁺? radicals, and to increase the relative Cu²⁺- and Fe³⁺-reducing levels. In the PTIO?-scavenging assay, its IC₅₀ values varied with pH. In the Fe²⁺-binding reaction, (+) taxifolin was found to yield a green solution with two UV-Vis absorbance peaks: λ_max =?433 nm (ε =5.2?×?10² L mol^?1 cm ^?1) and λ_max =?721 nm (ε?=?5.1?×?10² L mol^?1 cm ^?1). These results indicate that (+) taxifolin can act as an effective ?OH-scavenger, protecting bmMSCs from ?OH-induced damage. Its ?OH-scavenging action consists of direct and indirect antioxidant effects. Direct antioxidation occurs via multiple pathways, including ET, PCET or HAT. Indirect antioxidation involves binding to Fe²⁺.     

A model of a MAPK•substrate complex in an active conformation: a computational and experimental approach

The mechanisms by which MAP kinases recognize and phosphorylate substrates are not completely understood. Efforts to understand the mechanisms have been compromised by the lack of MAPK-substrate structures. While MAPK-substrate docking is well established as a viable mechanism for bringing MAPKs and substrates into close proximity the molecular details of how such docking promotes phosphorylation is an unresolved issue. In the present study computer modeling approaches, with restraints derived from experimentally known interactions, were used to predict how the N-terminus of Ets-1 associates with ERK2. Interestingly, the N-terminus does not contain a consensus-docking site ((R/K)_2-3-X_2-6-Φ_A-X-Φ_B, where Φ is aliphatic hydrophobic) for ERK2. The modeling predicts that the N-terminus of Ets-1 makes important contributions to the stabilization of the complex, but remains largely disordered. The computer-generated model was used to guide mutagenesis experiments, which support the notion that Leu-11 and possibly Ile-13 and Ile-14 of Ets-1 1-138 (Ets) make contributions through binding to the hydrophobic groove of the ERK2 D-recruiting site (DRS). Based on the modeling, a consensus-docking site was introduced through the introduction of an arginine at residue 7, to give the consensus ⁷RK-X₂-Φ_A-X-Φ_B ¹³. This results in a 2-fold increase in k _cat/K _m for the phosphorylation of Ets by ERK2. Similarly, the substitution of the N-terminus for two different consensus docking sites derived from Elk-1 and MKK1 also improves k _cat/K _m by two-fold compared to Ets. Disruption of the N-terminal docking through deletion of residues 1-23 of Ets results in a 14-fold decrease in k _cat/K _m, with little apparent change in k _cat. A peptide that binds to the DRS of ERK2 affects K _m, but not k _cat. Our kinetic analysis suggests that the unstructured N-terminus provides 10-fold uniform stabilization of the ground state ERK2•Ets•MgATP complex and intermediates of the enzymatic reaction.     

Calorie restriction increases cerebral mitochondrial respiratory capacity in a NO•-mediated mechanism: impact on neuronal survival

Calorie restriction (CR) enhances animal life span and prevents age-related diseases, including neurological decline. Recent evidence suggests that a mechanism involved in CR-induced life-span extension is NO^?-stimulated mitochondrial biogenesis. We examine here the effects of CR on brain mitochondrial content. CR increased eNOS and nNOS and the content of mitochondrial proteins (cytochrome c oxidase, citrate synthase, and mitofusin) in the brain. Furthermore, we established an in vitro system to study the neurological effects of CR using serum extracted from animals on this diet. In cultured neurons, CR serum enhanced nNOS expression and increased levels of nitrite (a NO^? product). CR serum also enhanced the levels of cytochrome c oxidase and increased citrate synthase activity and respiratory rates in neurons. CR serum effects were inhibited by L-NAME and mimicked by the NO^? donor SNAP. Furthermore, both CR sera and SNAP were capable of improving neuronal survival. Overall, our results indicate that CR increases mitochondrial biogenesis in a NO^?-mediated manner, resulting in enhanced reserve respiratory capacity and improved survival in neurons.