Characterization of an efficient N-oxygenase from Saccharothrix sp. and its application in the synthesis of azomycin

BACKGROUND

The nitro group constitutes a significant functional moiety within numerous valuable substances, such as nitroimidazoles, a class of antimicrobial drugs exhibiting broad spectrum activity. Conventional chemical methods for synthesizing nitro compounds suffer from harsh conditions, multiple steps, and environmental issues. Biocatalysis has emerged as a promising alternative to overcome these drawbacks, with certain enzymes capable of catalyzing nitro group formation gradually being discovered in nature. Nevertheless, the practical application is hindered by the restricted diversity and low catalytic activity exhibited by the reported nitrifying enzymes.

RESULTS

A novel N-oxygenase SaRohS harboring higher catalytic capability of transformation 2-aminoimidazole to azomycin was characterized from Saccharothrix sp. Phylogenetic tree analysis revealed that SaRohS belongs to the heme-oxygenase-like diiron oxygenase (HDOs) family. SaRohS exhibited optimal activity at pH 5.5 and 25 ℃, respectively. The enzyme maintained relatively stable activity within the pH range of 4.5 to 6.5 and the temperature range of 20 ℃ to 35 ℃. Following sequence alignment and structural analysis, several promising amino acid residues were meticulously chosen for catalytic performance evaluation. Site-directed mutations showed that threonine 75 was essential for the catalytic activity. The dual mutant enzyme G95A/K115T exhibited the highest catalytic efficiency, which was approximately 5.8-fold higher than that of the wild-type and 22.3-fold higher than that of the reported N-oxygenase KaRohS from Kitasatospora azatica. The underlying catalytic mechanism was investigated through molecular docking and molecular dynamics. Finally, whole-cell biocatalysis was performed and 2-aminoimidazole could be effectively converted into azomycin with a reaction conversion rate of 42% within 14 h.

CONCLUSIONS

An efficient N-oxygenase that catalyzes 2-aminoimidazole to azomycin was screened form Saccharothrix sp., its phylogenetics and enzymatic properties were analyzed. Through site-directed mutation, enhancements in catalytic competence were achieved, and the molecular basis underlying the enhanced enzymatic activity of the mutants was revealed via molecular docking and dynamic simulation. Furthermore, the application potential of this enzyme was assessed through whole cell biocatalysis, demonstrating it as a promising alternative method for azomycin production.

A High-Specific-Activity L-aspartate-α-Decarboxylase from Bacillus aryabhattai Gel-09 and Site-Directed Mutation to Improve Its Substrate Tolerance

L-aspartate-α-decarboxylase (ADC) can recognize L-aspartic acid specifically and catalyze the decarboxylation of L-aspartic acid to β-alanine. In this study, a novel L-aspartate-α-decarboxylase (BaADC) with high specific activity from Bacillus aryabhattai Gel-09 was heterologously expressed and characterized. It exhibited optimal enzyme activity at pH 5.5 and 75 °C, and its specific activity was 33.9 U/mg. To improve the substrate tolerance of BaADC, site-directed mutation was used to construct variants. The optimal variant BaADC_I88M exhibited higher pH stability and thermostability, with 1.2-fold increase in catalytic efficiency. Moreover, through the fed-batch method, the conversion of L-aspartic acid to β-alanine catalyzed by BaADC_I88M reached 98.6% (128.67 g/L) at 12 h, which was 1.42-fold that of the wild-type enzyme. The mechanism of improved substrate tolerance was interpreted by molecular dynamics simulation and structural analysis, which revealed that the local conformational change in the active pocket could promote correct protonation. These results suggested that BaADC and its variant are potential candidates for use in the industrial production of β-alanine.

An efficient chemoenzymatic cascade strategy for transforming biomass into furfurylamine with lobster shell-based chemocatalyst and mutated ω-transaminase biocatalyst in methyl isobutyl ketone-water

To date, an efficient process for manufacturing valuable furan compounds from available renewable resources has gained great attention via a chemoenzymatic route. In this study, a sulfonated tin-loaded heterogeneous catalyst CLUST-Sn-LS using lobster shell as biobased carrier was prepared to convert corncob (75.0 g/L) into furfural (122.5 mM) at 170 °C for 30 min in methyl isobutyl ketone (MIBK)-H₂O biphasic system (2:1, v/v). To improve furfurylamine yield, a novel recombinant E. coli TFTS harboring robust mutant Aspergillus terreus ω-transaminase [hydrophilic threonine (T) at position 130 was site-directed mutated to hydrophobic phenylalanine (F)] was constructed to transform 300-500 mM furfural into furfurylamine (90.1-93.6 % yield) at 30 °C and pH 7.5 in MIBK-H₂O. Corncob was converted to furfurylamine in MIBK-H₂O with a high productivity of 0.461 g furfurylamine/(g xylan). This constructed chemoenzymatic method coupling bio-based chemocatalyst CLUST-Sn-LS and mutant ω-transaminase biocatalyst in a biphasic system could efficiently convert lignocellulose into furfurylamine.

Site-Directed Mutation of Salicylate Decarboxylase Gene and Mechanism of Ginkgo Acid Decarboxylation

Ginkgo seed is an important Chinese medicine and food resource in China, but the toxicity of ginkgo acid in it limits its application. Previous studies have found that salicylic acid decarboxylase (Sdc) has a decarboxylation degradation effect on ginkgo acid. In order to improve the decarboxylation ability of Sdc to Ginkgo acid, 11 residues of the Sdc around the substrate (salicylic acid) were determined as mutation targets according to the analysis of crystal structure of Sdc (PDB ID:6JQX), from Trichosporon moniliiforme WU-0401, and a total of 30 single point mutant enzymes and one compound mutant enzyme were obtained. With Ginkgo acid C15:1 as the substrate, it was found from activity assay that Sdc-Y64T and Sdc-P191A had higher decarboxylation activity, which increased by 105.18% and 116.74% compared with that of wild type Sdc, respectively. The optimal pH for Sdc Y64T and Sdc-P191A to decarboxylate Ginkgo acid C15:1 was 5.5, which is the same as the wild type Sdc. The optimal temperature of Sdc-P191A was 50 °C, which was consistent with that of the wild type Sdc, but the optimal temperature of the mutant Sdc-Y64T was 40 °C, which was 10 °C lower than that of wild type Sdc.

Characterization of aspartokinase double mutants using a combination of experiments and simulations

Aspartokinase (AK) is synergistically suppressed by Thr and Lys in the Corynebacterium metabolic pathway. Site-directed mutations can significantly improve AK inhibition. Our previous studies confirmed that sites 379 and 380 were important sites affecting enzyme activity, so we further screen the double mutants with excellent enzymatic properties from sites 379 and 380, and discuss the difference of enzyme activity between the double mutants and single mutants. Here, a double mutant, T379L/A380 M, with improved enzyme activity (2.74-fold) was obtained. Enzymatic property experiments showed that the optimum temperature of T379L/A380 M increased from 26 °C (recombinant Escherichia coli; WT-AK) to 45 °C and that the optimal pH decreased from 8.0 (WT-AK) to 7.5. Further, the half-life decreased from 4.5 to 3.32 h. These enzymatic properties were better than other mutant strains. Inhibition was diminished with low concentrations of Lys, and Lys + Thr presented an activating role. Subsequently, the reasons for the improved AK enzyme activity were illustrated with microscale thermophoresis (MST) experiments and molecular dynamic (MD) simulation by measuring ligand affinity and AK conformational changes. MST showed that the affinity between T379L/A380 M and Lys decreased, but the affinity between T379L/A380 M and Asp increased, promoting T379L/A380 M enzyme activity. MD experiments showed that T379L/A380 M enhanced the Asp-ATP affinity and catalyzed the transfer of residues S192 and D193 to Asp, promoting T379L/A380 M enzyme activity. However, the mutation did not cause fluctuations in the substrate Asp and ATP pockets. This might be why the enzyme activity was inferior to that of the single mutants (T379L and A380 M).

Differences in ASP1 expression and binding dynamics to queen mandibular pheromone HOB between Apis mellifera and Apis cerana workers reveal olfactory adaptation to colony organization

The eastern Apis cerana (Ac) and the western Apis mellifera (Am) are two closely related and most economically valuable honeybee species managed extensively worldwide. However, how worker bees of Ac and Am are adapted to their colony organization remains to be uncovered. Here, we found that the expression level of gene encoding antennae-specific proteins 1 (ASP1, a key regulator in recognizing queen mandibular pheromone) was positively correlated with the colony sizes in both bee species, and the expression level in Am was higher than that in Ac, suggesting that ASP1 may play an important role in maintaining colony homeostasis. Using competitive binding assay, molecular docking, and site-directed mutagenesis, we then confirmed the good binding affinities of both Ac-ASP1 and Am-ASP1 to methyl p-hydroxy benzoate (HOB), and Val115 was the key amino acid. However, the affinity of Am-ASP1 was stronger than that of Ac-ASP1. EAG analysis further demonstrated that antennae of Am worker bees had faster depolarization and repolarization in response to HOB stimulation. Taken together, these findings indicate that the differences in expression levels and binding dynamics allow ASP1 recognizing HOB to potentially serve as a specific regulator of colony organization in Ac and Am.

Characterizing of a new α-agarase AgaE from Thalassomonas sp. LD5 and probing its catalytically essential residues

A new α-agarase AgaE belonging to glycoside hydrolase (GH) family 96 was identified and cloned from marine bacterium Thalassomonas sp. LD5. AgaE consists of 926 amino acids with a theoretical molecular mass of 97 kDa. The optimum temperature and pH for recombinant AgaE were 35 °C and 7.0, respectively. In contrast to known α-agarases, the activity of AgaE does not depend on Ca²⁺, but on Na⁺. Thin-layer chromatography and ¹³C NMR analysis revealed that AgaE endohydrolytic of agarose to produce agarotetraose and agarohexaose as the final main products. Extensive site-directed mutagenesis studies on the conserved carboxylic amino acids of GH96 revealed two essential amino acids for AgaE, D779 and D781. Replacing D779 with G779 leads to complete inactivation of the enzyme, while D781G results in 70% loss of activity. Later studies showed that site D781 involved in the binding of Na⁺, and its mutation raised the optimal concentration of Na⁺ 4 times higher than that of the wild type. However, attempts to rescue the mutant's activities with sodium azide were failed. Kinetic parameters comparison of AgaE, AgaD, another α-agarase from LD5, and their mutants revealed that the former aspartic acid plays critical role in the catalysis.

Site-specific labeling and functional efficiencies of human fibroblast growth Factor-1 with a range of fluorescent dyes in the flexible N-Terminal region and a rigid β-turn region

Human fibroblast growth factor 1 (hFGF1) binding to its receptor and heparin play critical roles in cell proliferation, angiogenesis and wound healing but is also implicated in cancer. Fluorescence imaging is a powerful approach to study such protein interactions, but it is not always obvious if the site chosen will be efficiently labeled, often relying on trial-and-error. To provide a more systematic approach towards an efficient site-specific labeling strategy, we labeled two structurally distinct regions of the protein - the flexible N-terminus and a rigid loop. Several dyes were chosen to cover the visible region and to investigate how the structure of the dye affects the labeling efficiency. Flexibility in either the protein labeling site or the dye structure was found to result in high labeling efficiency, but flexibility in both resulted in a significant decrease in labeling efficiency. Conversely, too much rigidity in both can result in dye-protein interactions that can aggregate the protein. Importantly, site-specifically labeling hFGF1 in these regions maintained biological activity. These results could be applicable to other proteins by considering the flexibility of both the protein labeling site and the dye structure.

Improving the catalytic efficiency and substrate affinity of a novel esterase from marine Klebsiella aerogenes by random and site-directed mutation

A novel esterase (EstKa) from marine Klebsiella aerogenes was characterized with hydrolytic activity against p-nitrophenyl caprylate (pNPC, C₈) under optimum conditions (50 °C and pH 8.5). After two rounds of mutagenesis, two highly potential mutants (I6E9 and L7B11) were obtained with prominent activity, substrate affinity and thermostability. I6E9 (L90Q/P96T) and L7B11 (A37S/Q100L/S133G/R138C/Q156R) were 1.56- and 1.65-fold higher than EstKa in relative catalytic efficiency. The influence of each amino acid on enzyme activity was explored by site-directed mutation. The mutants Pro96Thr and Gln156Arg showed 1.29- and 1.48-fold increase in catalytic efficiency (Kcat/Km) and 54.4 and 36.2% decrease in substrate affinity (Km), respectively. The compound mutant Pro96Thr/Gln156Arg exhibited 68.9% decrease in Km and 1.41-fold increase in Kcat/Km relative to EstKa. Homology model structure analysis revealed that the replacement of Gln by hydrophilic Arg on the esterase surface improved the microenvironment stability and the activity. The replacement of Pro by Thr enabled the esterase enzyme to retain 90% relative activity after 3 h incubation at 45 °C. Structural analysis confirmed that the formation of a hydrogen bond leads to a notable increase of catalytic efficiency under high temperature conditions.

Development of CRISPR-Cas9 genome editing system in Talaromyces marneffei

Talaromyces marneffei is an important pathogenic thermally dimorphic fungus causing systemic talaromycosis mainly prevalent in Southeast Asia. The dimorphic transition between mycelium and yeast is considered crucial for the pathogenicity of T. marneffei. However, the lack of genetic toolbox has been a major impediment for understanding its pathogenicity. Here a CRISPR-Cas9 system was developed to facilitate genetic manipulations in this organism. In this study, the CRISPR-Cas9 gene editing system uses a native U6 snRNA promoter from T. marneffei to drive the expression of sgRNA. Employing this system and PEG-mediated protoplast transformation, the sakA gene was mutated. Sanger sequencing confirmed nearly 40% site-directed mutation rate. The phenotype analysis confirmed the sakA gene function in T. marneffei dimorphic transition. Our study provided a powerful genome-manipulating tool, which could accelerate studies on T. marneffei for further revealing the mechanisms of its pathogenicity.

A Novel Glucose-Tolerant GH1 β-Glucosidase and Improvement of Its Glucose Tolerance Using Site-Directed Mutation

A novel GH1 β-glucosidase gene (bgla) from marine bacterium was sequenced and expressed in Escherichia coli. After purification by Ni²⁺ affinity chromatography, the recombinant protein was characterized. The purified recombinant enzyme showed maximum activity at 40 °C, pH 7.5 and was stable between temperatures that range from 4 to 30 °C and over the pH range of 6-10. The enzyme displayed a high tolerance to glucose and maximum stimulation at the presence of 100 mM glucose. To improve glucose tolerance of the enzyme, a site-directed mutation (f171w) was introduced into β-glucosidase. The recombinant F171W showed a higher glucose tolerance than the wild type and maintained more than 40% residual activity at the presence of 4 M glucose. Additionally, the recombinant enzymes showed notable tolerance to ethanol. These properties suggest the enzymes may have potential applications for the fermentation of lignocellulosic sugars and the production of biofuels.

Biochemical characterization and evolutionary analysis of a novel pectate lyase from Aspergillus parasiticus

In this study, a novel pectate lyase (ApPel1) was identified and characterized from Aspergillus parasiticus. The ApPel1 hydrolysed oligogalacturonides (OGs) effectively and produced 4,5-unsaturated OGs from low-methoxyl (LM) pectin, with DP 2 to DP 5 as the major products. Furthermore, the multiple sequence alignments, structure model and phylogenetic analyses of the ApPel1 indicated that its catalytic active sites were highly conserved with other pectin lyases (PLs) and the Ca²⁺ binding amino acid residues are different compared with pectate lyases (Pels). N187D, N191D and N187D/N191D mutants were constructed to test for both Ca²⁺ binding properties and the effects on catalytic ability. The three mutations sharply decreased the activity of ApPel1 and Ca²⁺ tolerance, indicating that the Ca²⁺ binding amino acid residues are different from the other Pels. Based on the sequence and structure comparison between PLs and Pels, and mutation analysis, the ApPel1 may be direct evolution from PLs. Thus, this enzyme has potential for use in producing unsaturated OGs for biological activity study, and contributes to an improved understanding of the evolutionary relationships between PLs and Pels.

Rational design of a new mutant of tobacco etch virus protease in order to increase the in vitro solubility

Background and purpose:

Tobacco etch virus (TEV) protease is a protease with high sequence specificity which is useful for the cleavage of fusion proteins. A major limitation of this enzyme is its relatively poor solubility. This study aimed to investigate the effects of some suggested mutations by online tools and molecular dynamics simulation to improve the solubility of TEV protease in vitro.

Experimental approach:

We designed a rational multi-stage process to determine the solubilizing mutations of TEV protease. At the first stage, all the possible mutations were predicted using online tools such as PoPMuSiC and Eris servers, in which five mutations include N23F, N23L, Q74L, Q74V, and Q74I were suggested for further studies. In the next step, the three dimensional structure of the wild type (WT) and the best mutations were subjected to molecular dynamic simulations to evaluate the dynamic behaviour of the obtained structures. The selected mutation was introduced into the structure using site-directed mutagenesis and expressed in Escherichia coli BL21DE3. After purification, solubility and activity of the purified mutant and WT-TEV proteases were assayed.

Findings /Results:

By considering the analysis of various factors such as structural and solubility properties, one mutant, N23F, was selected for in vitro studies which led to a 1.5 times increase in the solubility compared to the WT while its activity was decreased somewhat.

Conclusion and implications:

We propose N23F mutation, according to computational and experimental analyses for TEV proteases which resulted in a 150% increase in solubility compared to the WT.

Efficient targeted mutation of genomic essential genes in yeast Saccharomyces cerevisiae

Targeted gene mutation by allelic replacement is important for functional genomic analysis and metabolic engineering. However, it is challenging in mutating the essential genes with the traditional method by using a selection marker, since the first step of essential gene knockout will result in a lethal phenotype. Here, we developed a two-end selection marker (Two-ESM) method for site-directed mutation of essential genes in Saccharomyces cerevisiae with the aid of the CRISPR/Cas9 system. With this method, single and double mutations of the essential gene ERG20 (encoding farnesyl diphosphate synthase) in S. cerevisiae were successfully constructed with high efficiencies of 100%. In addition, the Two-ESM method significantly improved the mutation efficiency and simplified the genetic manipulation procedure compared with traditional methods. The genome integration and mutation efficiencies were further improved by dynamic regulation of mutant gene expression and optimization of the integration modules. This Two-ESM method will facilitate the construction of genomic mutations of essential genes for functional genomic analysis and metabolic flux regulation in yeasts. KEY POINTS: • A Two-ESM strategy achieves mutations of essential genes with high efficiency of 100%. • The optimized three-module method improves the integration efficiency by more than three times. • This method will facilitate the functional genomic analysis and metabolic flux regulation.

PEP-FOLD design, synthesis, and characteristics of finger-like polypeptides

Polypeptides with finger-like structures can often intercalate into the grooves of DNA, thereby affecting DNA repair or activating gene transcription, both of which are crucial for the regulation of physiological processes. Their conserved amino acid sequence and simple structure have provided useful elements for the design and assembly of functional molecules. In this paper, using the C₂H₂ zinc finger domain and the PEP-FOLD3 online simulation platform 11 polypeptides containing 22 amino acid residues were designed. In addition, the CD spectroscopy was combined with the fluorescence spectroscopy to study the polypeptide structures and their interaction with DNA. Results showed that although addition of zinc ions affected the polypeptide structure, particularly of the polypeptides A4, B1, and B3, zinc ion was not an essential factor for increasing polypeptide-DNA interactions. Our study revealed an increase in the interaction strength between mutated polypeptides and DNA, suggesting that mutations disrupt polypeptide structure, and polypeptides interact with DNA by groove and electrostatic binding. Mutations at the 12th and 15th amino acid residues had the greatest effect. The stronger binding between A2 or B2 and DNA indicates that the polypeptide has a spatial structure that can stably interact with DNA. The structure and characteristics of these polypeptide domains can provide information for the design and development of new polypeptide functional molecules, which could have potential significance and applications. However, this information also suggests that there are many challenges facing polypeptide design due to the synergistic effects between the side chains of amino acid residues.

Lys-Arg mutation improved the thermostability of Bacillus cereus neutral protease through increased residue interactions

Neutral proteases have broad application as additives in modern laundry detergents and therefore, thermostability is an integral parameter for effective production of protein crystals. To improve thermostability, the contribution of individual residues of Bacillus cereus neutral protease was examined by site-directed mutagenesis. The Lys11Arg and Lys211Arg mutants clearly possessed improved thermostabilities (T_m were 63 and 61 °C respectively) compared to the wild-type (T_m was 60 °C). MD simulations further revealed that the mutants had low RMSD and RMSF values compared to wild-type BCN indicating increased stability of the protein structure. Lys11Arg mutant particularly possessed the lowest RMSD values due to increased residue interactions, which resulted in enhanced thermostability. The mutants also displayed strong stability to most inhibitors, organic solvents and surfactants after incubation for 1 h. This study demonstrated Lys-Arg mutation enhanced thermostability of BCN and thus provides insight for engineering stabilizing mutations with improved thermostability for related proteins.

Two amino acid changes in the R3 repeat cause functional divergence of two clustered MYB10 genes in peach

R2R3-MYB genes play a pivotal role in regulating anthocyanin accumulation. Here, we report two tandemly duplicated R2R3-MYB genes in peach, PpMYB10.1 and PpMYB10.2, with the latter showing lower ability to induce anthocyanin accumulation than the former. Site-directed mutation assay revealed two amino acid changes in the R3 repeat, Arg/Lys⁶⁶ and Gly/Arg⁹³, responsible for functional divergence between these two PpMYB10 genes. Anthocyanin-promoting activity of PpMYB10.2 was significantly increased by a single amino acid replacement of Arg⁹³ with Gly⁹³. However, either the Gly⁹³ → Arg⁹³ or Arg⁶⁶ → Lys⁶⁶ substitutions alone showed little impact on anthocyanin-promoting activity of PpMYB10.1, but simultaneous substitutions caused a significant decrease. Reciprocal substitution of Arg/Gly⁹³ could significantly alter binding affinity to PpbHLH3, while the Arg⁶⁶ → Lys⁶⁶ substitution is predicted to affect the folding of the MYB DNA-binding domain, instead of PpbHLH3-binding affinity. Overall, the change of anthocyanin-promoting activity was accompanied with that of bHLH-binding affinity, suggesting that DNA-binding affinity of R2R3-MYBs depends on their bHLH partners. Our study is helpful for understanding of functional evolution of R2R3-MYBs and their interaction with DNA targets.

Improvement of alkalophilicity of an alkaline xylanase Xyn11A-LC from Bacillus sp. SN5 by random mutation and Glu135 saturation mutagenesis

BACKGROUND

Family 11 alkaline xylanases have great potential economic applications in the pulp and paper industry. In this study, we would improve the alkalophilicity of family 11 alkaline xylanase Xyn11A-LC from Bacillus sp. SN5, for the better application in this field.

RESULTS

A random mutation library of Xyn11A-LC with about 10,000 clones was constructed by error-prone PCR. One mutant, M52-C10 (V116A and E135V), with improved alkalophilicity was obtained from the library. Site-directed mutation showed that the mutation E135V was responsible for the alkalophilicity of the mutant. The variant E135V shifted the optimum pH of the wild-type enzyme from 7.5 to 8.0. Compared to the relative activities of the wild type enzyme, those of the mutant E135V increased by 17.5, 18.9, 14.3 and 9.5 % at pH 8.5, 9.0, 9.5 and 10.0, respectively. Furthermore, Glu135 saturation mutagenesis showed that the only mutant to have better alkalophilicity than E135V was E135R. The optimal pH of the mutant E135R was 8.5, 1.0 pH units higher than that of the wild-type. In addition, compared to the wild-type enzyme, the mutations E135V and E135R increased the catalytic efficiency (k _cat/K _m) by 57 and 37 %, respectively. Structural analysis showed that the residue at position 135, located in the eight-residue loop on the protein surface, might improve the alkalophilicity and catalytic activity by the elimination of the negative charge and the formation of salt-bridge.

CONCLUSIONS

Mutants E135V and E135R with improved alkalophilicity were obtained by directed evolution and site saturation mutagenesis. The residue at position 135 in the eight-residue loop on the protein surface was found to play an important role in the pH activity profile of family 11 xylanases. This study provided alkalophilic mutants for application in bleaching process, and it was also helpful to understand the alkaline adaptation mechanism of family 11 xylanases.

Separation of enzymatic functions and variation of spin state of rice allene oxide synthase-1 by mutation of Phe-92 and Pro-430

Rice allene oxide synthase-1 mutants carrying F92L, P430A or F92L/P430A amino acid substitution mutations were constructed, recombinant mutant and wild type proteins were purified and their substrate preference, UV-vis spectra and heme iron spin state were characterized. The results show that the hydroperoxide lyase activities of F92L and F92L/P430A mutants prefer 13-hydroperoxy substrate to other hydroperoxydienoic acids or hydroperoxytrienoic acids. The Soret maximum was completely red-shifted in P430A and F92L/P430A mutants, but it was partially shifted in the F92L mutant. ESR spectral data showed that wild type, F92L and P430A mutants occupied high and low spin states, while the F92L/P430A mutant occupied only low spin state. The extent of the red shift of the Soret maximum increased as the population of low spin heme iron increased, suggesting that the spectral shift reflects the high to low transition of heme iron spin state in rice allene oxide synthase-1. Relative to wild type allene oxide synthase-1, the hydroperoxide lyase activities of F92L and F92L/P430A are less sensitive to inhibition by imidazole with (13S or 9S)-hydroperoxydienoic acid as substrate and more sensitive than wild type with (13S)-hydroperoxytrienoic acid as substrate. Our results suggest that hydroperoxydienoic acid is the preferred substrate for the hydroperoxide lyase activity and (13S)-hydroperoxytrienoic acid is the preferred substrate for allene oxide synthase activity of allene oxide synthase-1.

An improved method for introducing site-directed point mutation into the Toxoplasma gondii genome using CRISPR/Cas9

Toxoplasma gondii is an obligate intracellular parasite in the phylum Apicomplexa. Due to the ease of genetic manipulations in T. gondii it serves as a model organism for intracellular parasites. We utilized CRISPR/Cas9, which can be designed to target a specific genomic locus, to introduce site-directed point mutations directly into the T. gondii genomes. This paper contains step-by-step protocols for: (1) designing the guide RNA sequence; (2) constructing the CRISPR/Cas9 construct for a target gene and preparing a donor sequence; and (3) transfecting the CRISPR/Cas9 modules into the parasite and selecting the parasite with the desired point mutation. In brief: T. gondii strains PRU∆ku80∆hxgprt or RH∆ku80∆hxgprt were nucleofected with pDHFR-SAG1::Cas9-U6::sgGeneA and a mutation donor sequence at a molar ratio of ~1:3. After 10days of 1μM pyrimethamine selection the parasite population was enriched for parasites with the desired point mutation. This technique was also applied to evaluate the importance of genes of interest by introducing either knock out or silence mutations at the same time and then tracking the population kinetics of the resultant T. gondii strains. In addition to previously established high efficient knock out and knock in strategies in Toxoplasma, the site directed point mutation technique presented in this manuscript provides another powerful tool set for T. gondii research.

Molecular cloning and expression analysis of a new bilin lyase: the cpcT gene encoding a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the β-subunit of phycocyanin in Arthrospira platensis FACHB314

To study the assembly of phycocyanin β subunit, the gene cpcT was first cloned from Arthrospira platensis FACHB314. To explore the function of cpcT, the DNA of phycocyanin β subunit and cpcT were transformed into Escherichia coli BL21 with the plasmid pET-hox1-pcyA, which contained the genes hemeoxygenase 1 (Hox1) and ferredoxin oxidoreductase (PcyA) needed to produce phycocyanobilin. The transformed strains showed specific phycocyanin fluorescence, and the fluorescence intensity was stronger than the strains with only phycocyanin β subunit, indicating that CpcT can promote the assembly of phycocyanin to generate fluorescence. To study the possible binding sites of apo-phycocyanin and phycocyanobilin, the Cys-82 and Cys-153 of the β subunit were individually mutated, giving two kinds of mutants. The results show that Cys-153 maybe the active site for β subunit binding to phycocyanobilins, which is catalyzed by CpcT in A. platensis FACHB314.

Mutant LV(476-7)AA of A-subunit of Enterococcus hirae V1-ATPase: High affinity of A3B3 complex to DF axis and low ATPase activity

Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble functional domain V₁ (A₃B₃DF) and an integral membrane domain V_o (ac), where V₁ and V_o domains are connected by a central stalk, composed of D-, F-, and d-subunits; and two peripheral stalks (E- and G-subunits). We identified 120 interacting residues of A₃B₃ heterohexamer with D-subunit in DF heterodimer in the crystal structures of A₃B₃ and A₃B₃DF. In our previous study, we reported 10 mutants of E. hirae V₁-ATPase, which showed lower binding affinities of DF with A₃B₃ complex leading to higher initial specific ATPase activities compared to the wild-type. In this study, we identified a mutation of A-subunit (LV^476-7AA) at its C-terminal domain resulting in the A₃B₃ complex with higher binding affinities for wild-type or mutant DF heterodimers and lower initial ATPase activities compared to the wild-type A₃B₃ complex, consistent with our previous proposal of reciprocal relationship between the ATPase activity and the protein-protein binding affinity of DF axis to the A₃B₃ catalytic domain of E. hirae V-ATPase. These observations suggest that the binding of DF axis at the contact region of A₃B₃ rotary ring is relevant to its rotation activity.