Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system.

Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli often results in a myriad of unpredictable issues with regard to protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as a valuable expression platform as a testbed for rapid prototyping expression parameters. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We applied a library of constructs with different combinations of promoters and rppA coding sequences to investigate the synergies between promoter and codon usage. Subsequently, we assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. More importantly, the choice of coding sequences and promoters impact protein expression synergistically, which should be considered for future efforts to use CFE for high-yield protein expression. The promoter strategy when applied to RppA was not completely correlated with that observed with GFP, indicating that different promoter strategies should be applied for different proteins. In vivo experiments suggest that there is correlation, but not complete alignment between expressing in cell free and in vivo. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs, which advances CFE as a tool for natural product research.

Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases.

The sugars streptose and dihydrohydroxystreptose (DHHS) are unique to the bacteria Streptomyces griseus and Coxiella burnetii, respectively. Streptose forms the central moiety of the antibiotic streptomycin, while DHHS is found in the O-antigen of the zoonotic pathogen C. burnetii. Biosynthesis of these sugars has been proposed to follow a similar path to that of TDP-rhamnose, catalyzed by the enzymes RmlA, RmlB, RmlC, and RmlD, but the exact mechanism is unclear. Streptose and DHHS biosynthesis unusually requires a ring contraction step that could be performed by orthologs of RmlC or RmlD. Genome sequencing of S. griseus and C. burnetii has identified StrM and CBU1838 proteins as RmlC orthologs in these respective species. Here, we demonstrate that both enzymes can perform the RmlC 3'',5'' double epimerization activity necessary to support TDP-rhamnose biosynthesis in vivo. This is consistent with the ring contraction step being performed on a double epimerized substrate. We further demonstrate that proton exchange is faster at the 3''-position than the 5''-position, in contrast to a previously studied ortholog. We additionally solved the crystal structures of CBU1838 and StrM in complex with TDP and show that they form an active site highly similar to those of the previously characterized enzymes RmlC, EvaD, and ChmJ. These results support the hypothesis that streptose and DHHS are biosynthesized using the TDP pathway and that an RmlD paralog most likely performs ring contraction following double epimerization. This work will support the elucidation of the full pathways for biosynthesis of these unique sugars.

Quantitative selenium speciation in feed by enzymatic probe sonication and ion chromatography-inductively coupled plasma mass spectrometry.

A rapid, sensitive and species preservative analytical method for the simultaneous determination of six selenium (Se) species has been developed. Enzymatic probe sonication (EPS) was investigated as a novel and alternative technology for the extraction of Se species from feed matrices and the results were compared with the conventional hot water extraction, enzymatic hydrolysis and sequential extraction. The critical parameters of EPS such as enzyme types, extraction time, temperature, ultrasonic power and sample/enzyme ratio were varied with control. The Se species were separated and quantitatively determined by ion chromatography-inductively coupled plasma mass spectrometry (IC-ICP-MS). Under current optimised conditions, six inorganic and organic Se species were completely separated within 15 min in a single chromatographic run. The spectral interferences from the argon plasma 40Ar2, 40Ar37Cl or 1H79Br were effectively removed by employing the kinetic energy discrimination (KED) mode. Quantitative extraction for total Se (>94.8%) and more than 89.0% for the sum of different Se chemical forms without species transformation were obtained in only 60 s by applying the EPS treatment using aqueous protease XIV. The limits of detection (LODs) and quantification (LOQs) for Se species were in the ranges of 0.21-0.56 µg kg-1 and 0.69-1.87 µg kg-1, respectively. The proposed method was successfully applied to the speciation of Se in several reference materials and feed samples collected from the markets and local farms.

Effective refolding of a cysteine rich glycoside hydrolase family 19 recombinant chitinase from Streptomyces griseus by reverse dilution and affinity chromatography.

Conventional refolding methods are associated with low yields due to misfolding and high aggregation rates or very dilute proteins. In this study, we describe the optimization of the conventional methods of reverse dilution and affinity chromatography for obtaining high yields of a cysteine rich recombinant glycoside hydrolase family 19 chitinase from Streptomyces griseus HUT6037 (SgChiC). SgChiC is a potential biocontrol agent and a reference enzyme in the study and development of chitinases for various applications. The overexpression of SgChiC was previously achieved by periplasmic localization from where it was extracted by osmotic shock and then purified by hydroxyapatite column chromatography. In the present study, the successful refolding and recovery of recombinant SgChiC (r-SgChiC) from inclusion bodies (IB) by reverse dilution and column chromatography methods is respectively described. Approximately 8 mg of r-SgChiC was obtained from each method with specific activities of 28 and 52 U/mg respectively. These yields are comparable to that obtained from a 1 L culture volume of the same protein isolated from the periplasmic space of E. coli BL21 (DE3) as described in previous studies. The higher yields obtained are attributed to the successful suppression of aggregation by a stepwise reduction of denaturant from high, to intermediate, and finally to low concentrations. These methods are straight forward, requiring the use of fewer refolding agents compared with previously described refolding methods. They can be applied to the refolding of other cysteine rich proteins expressed as inclusion bodies to obtain high yields of actively folded proteins. This is the first report on the recovery of actively folded SgChiC from inclusion bodies.

Cloning and identification of the Frigocyclinone biosynthetic gene cluster from Streptomyces griseus strain NTK 97.

Frigocyclinone is a novel antibiotic with antibacterial and anticancer activities. It is produced by both Antarctica-derived Streptomyces griseus NTK 97 and marine sponge-associated Streptomyces sp. M7_15. Here, we first report the biosynthetic gene cluster of frigocyclinone in the S. griseus NTK 97. The frigocyclinone gene cluster spans a DNA region of 33-kb which consists of 30 open reading frames (ORFs), encoding minimal type II polyketide synthase, aromatase and cyclase, redox tailoring enzymes, sugar biosynthesis-related enzymes, C-glycosyltransferase, a resistance protein, and three regulatory proteins. Based on the bioinformatic analysis, a biosynthetic pathway for frigocyclinone was proposed. Second, to verify the cloned gene cluster, CRISPR-Cpf1 mediated gene disruption was conducted. Mutant with the disruption of beta-ketoacyl synthase encoding gene frig20 fully loses the ability of producing frigocyclinone, while inactivating the glycosyltransferase gene frig1 leads to the production of key intermediate of anti-MRSA anthraquinone tetrangomycin.

Molecular causes for the increased stickiness of cooked non-glutinous rice by enzymatic hydrolysis of the grain surface protein.

Non-glutinous rice has higher amylose content but less sticky texture than glutinous rice. In this study, by soaking two non-glutinous rice with protease solution, rice stickiness is significantly increased and equivalent to that of glutinous rice. By exploring starch leaching behavior during rice cooking, we find: (i) total solids and amylopectin amount in the leachate are significantly increased by raising the protease concentration during the soaking treatment; (ii) molecular size and chain-length distribution (CLD) of leached starch from these protease-treated rice (PTR) significantly differed from the corresponding native starch; (iii) strong correlations between rice stickiness, amylopectin amount and the proportion of short amylopectin chains with degree of polymerization (DP) <36 in the leachate are established. The possible molecular mechanism for the increased stickiness of treated non-glutinous rice is put forward to explain the above result. This study could broaden the applications of non-glutinous rice for rice industry.

An Innovative Approach to the Preparation of Plasma Samples for UHPLC-MS Analysis.

A new sample processing method for analyzing flavonol metabolites in plasma using enzymatic proteolysis was developed and validated. Four endopeptidases were examined regarding their influence on the analyte recovery of quercetin-3- O-glucuronide (Q3GlcA). Methanol was added to inactivate and precipitate the enzymes, and samples were concentrated via evaporation prior to UHPLC-MS analysis. Quercetin-3- O-rutinoside (Q3Rut) was used as an internal standard. The selectivity and accuracy of the established UHPLC-ESI-MS n method showed a coefficient of variation (CV) of the repeatability of the measuring instrument of 1.7% for Q3GlcA. The average recovery of Q3GlcA was approximately 67% with an interday method precision of 24% and r = 46.9 as its repeatability. Therefore, enzymatic proteolysis has proven to be a suitable alternative to the methods previously described in the literature, such as solid-phase extraction (SPE). Still, the method has only been validated for Q3GlcA, but its applicability to other substance classes seems possible.

Simultaneous extraction and determination of mono-/polyglutamyl folates using high-performance liquid chromatography-tandem mass spectrometry and its applications in starchy crops.

Folates are typically present in polyglutamyl form in organisms. In traditional extraction methods, polyglutamyl folates are hydrolyzed to monoglutamates, sacrificing valuable information. To advance folate metabolism research, we developed an accurate, sensitive, and reproducible extraction method for polyglutamyl folate species in maize, the main crop in most parts of the world. Twelve folates, including six polyglutamyl folates, were simultaneously determined in maize for the first time using high-performance liquid chromatography-tandem mass spectrometry. The glutamation states of the folates were protected by boiling, which inactivated the native conjugases. α-Amylase and protease were added to obtain better recoveries and decrease difficulties in centrifugation and filtration. The recoveries (n = 5) of six polyglutamyl folates were between 80.5 and 101%. All calibration curves showed good linear regression (r2 ≥ 0.994) within the working range. The instrumental limits of detection and quantitation ranged from 0.070 to 2.4 ng/mL and 0.22 to 8.0 ng/mL, respectively. Intra- and inter-day precision was below 7.81% and 11.9%, respectively (n = 5). Using this method, changes in poly- and monoglutamyl folates during maize germination were determined for the first time. The results suggest that folates were largely synthesized as germination initiated, and 5-methyltetrahydrofolate was the most abundant species. Tetraglutamyl 5-methyltetrahydrofolate contributed more than 50% of the 5-methyltetrahydrofolate species. Inverse changes in contents of 5,10-methenyltetrahydrofolate, and 10-formyl folic acid, monoglutamate, and diglutamate of 5-formyltetrahydrofolate were also observed, indicating potential regulation. Additionally, polyglutamyl folates in sweet potatoes were determined using this method, indicating its applications in starchy crops.

Enzyme-catalyzed regio-selective demethylation of papaverine by CYP105D1.

OBJECTIVES: To investigate the regio-selective demethylation of papaverine by CYP105D1 and develop a whole-cell biocatalytic system for the preparative synthesis of 6-O-demethyl-papaverine. RESULTS: CYP105D1 from Streptomyces griseus ATCC 13273 was used for the regioselective demethylation of papaverine at C-6 using putidaredoxin reductase (PDR) and putidaredoxin (Pdx) as the electron transport system. The Km value of CYP105D1 towards papaverine was estimated to be 92.24 µM. Furthermore, a CYP105D1-based whole-cell system was established in E. coli BL21(DE3). The whole cell biotransformation condition was optimized as 25 °C, pH 7.5, 8 g (cell dry weight) L-1 whole cell biomass and 3% (v/v) PEG-200 as cosolvent. Under the optimal condition, the conversion yield of papaverine reached to 61.15% within 24 h. CONCLUSIONS: The selective demethylation of papaverine by CYP105D1 was accomplished. The CYP105D1-based whole-cell biocatalyst has a potential used for the efficient synthesis of 6-O-demethyl-papaverine.

Regio- and enantioselective O-demethylation of tetrahydroprotoberberines by cytochrome P450 enzyme system from Streptomyces griseus ATCC 13273.

Tetrahydroprotoberberines (THPBs), a class of naturally occurring isoquinoline alkaloids, contain substituent methoxyl or hydroxyl groups which play a significant role in the pharmacological properties of these molecules. In this study, we report a biocatalytic strategy for selective O-demethylation of THPBs. CYP105D1, a cytochrome P450 from Streptomyces griseus ATCC 13273, exhibited markedly regioselective demethylation of nonhydroxyl-THPBs and monohydroxyl-THPBs on the D-ring. A possible binding mode of THPBs with CYP105D1 was investigated by docking analysis, and the results revealed that the D-rings of THPBs were with the minimum distance to the heme iron. Tetrahydropalmatine was used as a model substrate and enantioselective demethylation was demonstrated. (S)-Tetrahydropalmatine was only demethylated at C-10, while (R)-tetrahydropalmatine was first demethylated at C-10 and then subsequently demethylated at C-9. The kcat/Km value for demethylation of (R)-tetrahydropalmatine by CYP105D1 was 3.7 times greater than that for demethylation of (S)-tetrahydropalmatine. Furthermore, selective demethylation of (S)-tetrahydropalmatine by the CYP105D1-based whole-cell system was demonstrated for the highly efficient production of (S)-corydalmine which has distinct pharmacological applications, such as providing relief from bone cancer pain and reducing morphine tolerance. Moreover, a homologous redox partner was identified to enhance the catalytic efficiency of the CYP105D1-based whole-cell system. This is the first enzymatic characterization of a cytochrome P450 that has regio- and enantioselective demethylation activity of THPBs for application purpose. The cytochrome P450 system could be a promising strategy for selective demethylation in the pharmaceutical industry.

Enzymatic hydrolysis of ionic liquid-extracted chitin.

Chitin, one of Nature's most abundant biopolymers, can be obtained by either traditional chemical pulping or by extraction using the ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate. The IL extraction and coagulation process provides access to a unique chitin, with an open hydrated gel-like structure. Here, enzymatic hydrolysis of this chitin hydrogel, dried shrimp shell, chitin extracted from shrimp shells using IL and then dried, and commercial chitin was carried out using chitinase from Streptomyces griseus. The enzymatic hydrolysis of shrimp shells resulted only in the monomer N-acetylglucosamine, while much higher amounts of the dimer (N,N'-diacetylchitobiose) compared to the monomer were detected when using all forms of 'pure' chitin. Interestingly, small amounts of the trimer (N,N',N''-triacetylchitotriose) were also detected when the IL-chitin hydrogel was used as substrate. Altogether, our findings indicate that the product distribution and yield are highly dependent on the substrate selected for the reaction and its hydrated state.

HPLC Determination of Total Tryptophan in Infant Formula and Adult/Pediatric Nutritional Formula Following Enzymatic Hydrolysis: Single-Laboratory Validation, First Action 2017.03.

A method for tryptophan (Trp) analysis designed to comply with AOAC Standard Method Performance Requirement 2014.013 is described. Unlike AOAC 988.15, which uses alkaline hydrolysis, this method uses enzymatic hydrolysis to release the Trp from the intact protein. The method achieves an LOQ of 0.18 mg/100 g Trp on a ready-to-feed basis with mean recoveries ranging from 93.8 to 104.9%. Repeatability ranged from 0.2 to 5.0%. Intermediate precision ranged from 1.0 to 6.9%. The analytical range was determined to be 0.18-300 mg/100 g, with linearity over eight calibration standard levels giving an average deviation from theoretical levels of 0.3%. No single calibration point had a deviation of >5.0%. Two standard reference materials (SRMs 1849a and 927e) were analyzed, and the average deviation from the certified value was 98.5% for SRM 1849a and 101.2% for SRM 927e. Sample preparation is very similar to existing methods in terms of time and complexity. The use of an internal standard reduces laboratory error and allows for reproducible results.

Protease sensitivity and redistribution of CD71 and glycophorin A on K562 cells.

Transmembrane proteins are delivered to plasma membrane from the endoplasmic reticulum and Golgi complex by vesicular transport along with the cytoskeletal network. Disruption of this process likely affects transmembrane protein expression. K562 cells were digested with Streptomyces griseus protease for different periods of time, and then re-cultured with different cytoskeletal and glycosylation inhibitors. Cell viability and surface expression of transferrin receptor (CD71) and glycophorin A (GPA) were analyzed before and after re-culture by flow cytometry. We found that digestion with protease almost completely removed extracellular CD71 and GPA but their expression recovered to the initial levels after re-culture for 8 h and 24 h, respectively. The microtubule depolymerizer colchicine promoted cell surface recovery of CD71 but inhibited that of GPA; the microtubule stabilizer paclitaxel inhibited cell surface recovery of CD71 but promoted that of GPA; the microfilament depolymerizer cytochalasin D had no effect on cell surface recovery of CD71 and GPA; the microfilament stabilizer phalloidin inhibited cell surface recovery of GPA. The glycosylation inhibitor tunicamycin inhibited the recovery of both CD71 and GPA, and BADGP inhibited the recovery of GPA. These studies show differential sensitivities of surface proteins on K562 cells to proteases, and suggest molecular mechanisms of transmembrane protein transport and cycling.

Deciphering the Nature of Enzymatic Modifications of Bacterial Cell Walls.

The major constituent of bacterial cell walls is peptidoglycan, which, in its crosslinked form, is a polymer of considerable complexity that encases the entire bacterium. A functional cell wall is indispensable for survival of the organism. There are several dozen enzymes that assemble and disassemble the peptidoglycan dynamically within each bacterial generation. Understanding of the nature of these transformations is critical knowledge for these events. Octasaccharide peptidoglycans were prepared and studied with seven recombinant cell-wall-active enzymes (SltB1, MltB, RlpA, mutanolysin, AmpDh2, AmpDh3, and PBP5). With the use of highly sensitive mass spectrometry methods, we described the breadth of reactions that these enzymes catalyzed with peptidoglycan and shed light on the nature of the cell wall alteration performed by these enzymes. The enzymes exhibit broadly distinct preferences for their substrate peptidoglycans in the reactions that they catalyze.

Synthesis of new hydrophilic rhodamine based enzymatic substrates compatible with droplet-based microfluidic assays.

Here we report the conception, synthesis and evaluation of new hydrophilic rhodamine-based enzymatic substrates for detection of peptidase activity compatible with high-throughput screening using droplet-based microfluidics.

Bioresolution of racemic phenyl glycidyl ether by a putative recombinant epoxide hydrolase from Streptomyces griseus NBRC 13350.

In order to produce enantiomerically pure epoxides for the synthesis of value-added chemicals, a novel putative epoxide hydrolase (EH) sgeh was cloned and overexpressed in pET28a/Escherichia coli BL21(DE3). The 1047 bp sgeh gene was mined from Streptomyces griseus NBRC 13350 genome sequence. The recombinant hexahistidyl-tagged SGEH was purified (16.6-fold) by immobilized metal-affinity chromatography, with 90% yield as a homodimer of 100 kDa. The recombinant E. coli whole cells overexpressing SGEH could kinetically resolve racemic phenyl glycidyl ether (PGE) into (R)-PGE with 98% ee, 40% yield, and enantiomeric ratio (E) of 20. This was achieved under the optimized reaction conditions i.e. cell/substrate ratio of 20:1 (w/w) at pH 7.5 and 20 °C in 10% (v/v) dimethylformamide (DMF) in a 10 h reaction. 99% enantiopure (R)-PGE was obtained when the reaction time was prolonged to 12 h with a yield of 34%. In conclusion, an economically viable and environment friendly green process for the production of enantiopure (R)-PGE was developed by using wet cells of E. coli expressing recombinant SGEH.

ß-Glucosidase from Streptomyces griseus: Nanoparticle immobilisation and application to alkyl glucoside synthesis.

A novel ß-glucosidase from Streptomyces griseus was cloned and overexpressed in E. coli. The purified ß-glucosidase (44 kDa) had a Km of 8.6 ± 0.5 mM and a Vmax of 217 ± 5.0 µmoles-1min-1mg at 37 °C, pH 7.2 with p-nitrophenyl-ß-D glucopyranoside as substrate. The enzyme was characterised in terms of pH optimum (pH 6.9), temperature optimum (69 °C) and the influence of solvents and effectors. Purified S. griseus ß-glucosidase was successfully immobilised, by simple absorption, onto zinc oxide (ZnO) nanoparticles without covalent modification. It remained tightly bound even after extensive washing and could be reused up to ten times without significant loss of activity. The immobilised enzyme had a higher optimum temperature and greater thermostability than the free enzyme. In immobilised form the enzyme readily catalysed the synthesis of alkyl glucosides.

Biosynthesis of optically pure chiral alcohols by a substrate coupled and biphasic system with a short-chain dehydrogenase from Streptomyces griseus.

The increasing demand for biocatalysts in synthesizing enantiomerically pure chiral alcohols results from the outstanding characteristics of enzymes in reaction, economic, ecological issues. Many carbonyl reductases for producing chiral alcohols have been reported but there is still a lack of good catalytic efficacies. Herein, five carbonyl reductases from different Streptomyces were discovered by the strategy of genome mining. These reductases were overexpressed, and we chose SgCR for further study as it owned better enzyme activity. This protein was purified to apparent homogeneity, and its amino acid sequence was analyzed in comparison with that of the reported SDRs. The biocatalytic properties of SgCR were investigated, and this enzyme was confirmed to have the ability to convert various prochiral ketones into highly optically active alcohols. SgCR exhibited the highest activity towards ethyl 4-chloro-3-oxobutanoate (COBE) and the corresponding product ethyl (S)-4-chloro-3-hydroxybutanoate ((S)-CHBE) was obtained with high yield and excellent e.e. value by optimizing the biphasic system. Eventually, using isopropanol as the co-substrate for NADH recycling in the substrate-coupled reaction, the yield and enantioselectivity of (S)-CHBE were obtained at the values of 90% and 99%, respectively. These results indicate that SgCR is a promising boicatalyst for the synthesis of chiral alcohols in industry.

Effect of Tea Catechins on Folate Analysis in Green Tea by Microbiological Assay.

Green tea is thought to be a primary source of folate in the Japanese diet, based on folate content analyzed by a microbiological assay. Green tea also contains high amount of catechins, in particular, epigallocatechin gallate (EGCg), which was demonstrated to be able to inhibit the digestive enzyme activities and microbial growth in the folate assay. In the present study, we examined whether tea catechins interfered with components of the folate assay for green tea. A marked inhibitory effect of EGCg on microbial growth was observed at an inhibitory concentration of higher than 10 µg/mL. Tea catechins without the galloyl moiety did not show an inhibitory effect. EGCg inhibited the activity of the three enzymes used for assay sample preparation at an inhibitory concentration of higher than 750 µg/mL for α-amylase, 1,000 µg/mL for protease, and 50 µg/mL for conjugase. However, with each step of the assay, the actual concentration of EGCg was decreased to below the inhibitory concentration of each analytical step. Lack of influence of EGCg on green tea folate assay was confirmed by an addition of folate standard in tea infusion. These results suggested that tea catechins have no practical impact on folate analysis in green tea, using the general microbiological assay.

Improved Production of Active Streptomyces griseus Trypsin with a Novel Auto-Catalyzed Strategy.

N-terminal sequences play crucial roles in regulating expression, translation, activation and enzymatic properties of proteins. To reduce cell toxicity of intracellular trypsin and increase secretory expression, we developed a novel auto-catalyzed strategy to produce recombinant trypsin by engineering the N-terminus of mature Streptomyces griseus trypsin (SGT). The engineered N-terminal peptide of SGT was composed of the thioredoxin, glycine-serine linker, His6-tag and the partial bovine trypsinogen pro-peptide (DDDDK). Furthermore, we constructed a variant TLEI with insertion of the artificial peptide at N-terminus and site-directed mutagenesis of the autolysis residue R145. In fed-batch fermentation, the production of extracellular trypsin activity was significantly improved to 47.4 ± 1.2 U·ml(-1) (amidase activity, 8532 ± 142.2 U·ml(-1) BAEE activity) with a productivity of 0.49 U·ml(-1)·h(-1), which was 329% greater than that of parent strain Pichia pastoris GS115-SGT. This work has significant potential to be scaled-up for microbial production of SGT. In addition, the N-terminal peptide engineering strategy can be extended to improve heterologous expression of other toxic enzymes.