Functional Characterization of a Regiospecific Sugar-O-Methyltransferase from Nocardia.

Methyltransferases transfer a methyl group to a diverse group of natural products, thus providing structural diversity, stability, and altered pharmacological properties to the molecules. A limited number of regiospecific sugar-O-methyltransferases are functionally characterized. Thus, discovery of such an enzyme could solve the difficulties of biological production of methoxy derivatives of glycosylated molecules. In the current study, a regiospecific sugar-O-methyltransferase, ThnM1, belonging to the biosynthetic gene cluster (BGC) of 1-(α-L-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene produced by Nocardia sp. strain CS682, was analyzed and functionally characterized. ThnM1 demonstrated promiscuity to diverse chemical structures such as rhamnose-containing anthraquinones and flavonoids with regiospecific methylation at the 2'-hydroxyl group of the sugar moiety. Compared with other compounds, anthraquinone rhamnosides were found to be the preferred substrates for methylation. Thus, the enzyme was further employed for whole-cell biotransformation using engineered Escherichia coli to produce a methoxy-rhamnosyl derivative of quinizarin, an anthraquinone derivative. The structure of the newly generated derivative from Escherichia coli fermentation was elucidated by liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopic analyses and identified as quinizarin-4-O-α-l-2-O-methylrhamnoside (QRM). Further, the biological impact of methylation was studied by comparing the cytotoxicity of QRM with that of quinizarin against the U87MG, SNU-1, and A375SM cancer cell lines. IMPORTANCE ThnM1 is a putative sugar-O-methyltransferase produced by the Nocardia sp. strain CS682 and is encoded by a gene belonging to the biosynthetic gene cluster (BGC) of 1-(α-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene. We demonstrated that ThnM1 is a promiscuous enzyme with regiospecific activity at the 2'-OH of rhamnose. As regiospecific methylation of sugars by chemical synthesis is a challenging step, ThnM1 may fill the gap in the potential diversification of natural products by methylating the rhamnose moiety attached to them.

UPLC-PDA coupled HR-TOF ESI/MS2 -based identification of derivatives produced by whole-cell biotransformation of epothilone A using Nocardia sp. CS692 and a cytochrome P450 overexpressing strain.

Epothilone A, a microtubule-stabilizing agent used as therapeutics for the treatment of cancers, was biotransformed into three metabolites using Nocardia sp. CS692 and recombinant Nocardia overexpressing a cytochrome P450 from Streptomyces venezuelae (PikC). Among three metabolites produced in the biotransformation reaction mixtures, ESI/MS2 analysis predicted two metabolites (M1 and M2) as novel hydroxylated derivatives (M1 is hydroxylated at the C-8 position and M2 is hydroxylated at C-10 position), each with an opened-epoxide ring in their structure. Interestingly, metabolite M3 lacks an epoxide ring and is known as deoxyepothilone A, which is also called epothilone C. Metabolite M1 was produced only in PikC overexpressing strain. The endogenous enzymes of Nocardia sp. catalyzed hydroxylation of epothilone A to produce metabolite M2 and removed epoxide ring to produce metabolite M3. All the metabolites were identified based on UV-vis analysis and rigorous ESI/MS2 fragmentation based on epothilone A standard. The newly produced metabolites are anticipated to display novel cytotoxic effects and could be subjects of further pharmacological studies.

Four-Step Pathway from Phenylpyruvate to Benzylamine, an Intermediate to the High-Energy Propellant CL-20.

Benzylamine is a commodity chemical used in the synthesis of motion-sickness treatments and anticonvulsants, in dyeing textiles, and as a precursor to the high-energy propellant CL-20. Because chemical production generates toxic waste streams, biosynthetic alternatives have been explored, recently resulting in a functional nine-step pathway from central metabolism (phenylalanine) in E. coli. We report a novel four-step pathway for benzylamine production, which generates the product from cellular phenylpyruvate using enzymes from different sources: a mandelate synthase (Amycolatopsis orientalis), a mandelate oxidase (Streptomyces coelicolor), a benzoylformate decarboxylase (Pseudomonas putida), and an aminotransferase (Salicibacter pomeroyi). This pathway produces benzylamine at 24 mg/L in 15 h (4.5% yield) in cultures of unoptimized cells supplemented with phenylpyruvate. Because the yield is low, supplementation with pathway intermediates is used to troubleshoot the design. This identifies conversion inefficiencies in the mandelate synthase-mediated synthesis of (S)-mandelic acid, and subsequent genome mining identifies a new mandelate synthase (Streptomyces sp. 1114.5) with improved yield. Supplementation experiments also reveal native redirection of ambient phenylpyruvate away from the pathway to phenylalanine. Overall, this work illustrates how retrosynthetic design can dramatically reduce the number of enzymes in a pathway, potentially reducing its draw on cellular resources. However, it also shows that such benefits can be abrogated by inefficiencies of individual conversions. Addressing these barriers can provide an alternative approach to green production of benzylamine, eliminating upstream dependence on chlorination chemistry.

Trilobatin ameliorates bone loss via suppression of osteoclast cell differentiation and bone resorptive function in vitro and in vivo.

AIM: Due to on-going safety concerns or lack of efficacy of currently used medications for the treatment of osteoporosis (OP), identifying new therapeutic agents is an important part of research. In the present study, potential anti-osteoporotic activity of a natural flavonoid glycoside, trilobatin (phloretin 4-O-glucoside, Tri) was evaluated. MATERIAL AND METHODS: Osteoclastic cells were established by treating the RAW264.7 macrophage cells with RANKL and ovariectomized (OVX) C57BL/6 female mice were used as an animal model of postmenopausal OP. Actin ring formation, expression levels of osteoclastogenic marker genes and bone resorptive proteins were measured by RT-PCR, western blot, or fluorometric assays. Bone mineral density (BMD) was determined by pDEXA densitometric measurement and serum osteoprotegerin (OPG) and RANKL were measured by ELISA. KEY FINDING: Tri (5-20 µM) significantly inhibited osteoclast formation and actin ring formation in RANKL-induced osteoclasts. Tri attenuated expression of osteoclastogenic genes (MMP-9 and cathepsin K), bone resorptive proteins (CA II and integrin ß3), and osteoclastogenic signalling proteins (TRAF6, p-Pyk2, c-Cbl, and c-Src). Oral administration of Tri to OVX mice augmented BMD and serum OPG/RANKL ratio. Interestingly, while Tri and phloretin aglycone (Phl) showed similar levels of in vitro anti-osteoclastogenic activity, Tri more potently ameliorated bone loss than Phl in OVX mice. SIGNIFICANCE: This study demonstrated that Tri inhibits osteoclastic cell differentiation and bone resorption by down-regulating the expression of osteoclastogenic marker genes and signalling proteins, bone resorptive proteins, and by augmenting serum OPG/RANKL ratio, suggesting that Tri can be a novel anti-osteoporotic compound for treating senile and postmenopausal OP.

Chryseobacterium antibioticum sp. nov. with antimicrobial activity against Gram-negative bacteria, isolated from Arctic soil.

A yellow-pigmented, non-motile, Gram-stain-negative, pleomorphic bacterium, designated RP-3-3T was obtained from soil sampled at the Arctic region in Cambridge Bay, NU, Canada. The strain is strictly aerobic, psychrotolerant, grow optimally at 15-20 °C and produces flexirubin type pigments. The strain is able to hydrolyse CM-cellulose, casein, starch and DNA. Strain RP-3-3T showed antimicrobial activity against Gram-negative pathogens. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RP-3-3T formed a lineage within the family Weeksellaceae and clustered as members of the genus Chryseobacterium. The closest members were Chryseobacterium shigense DSM 17126T (98.7% sequence similarity), Chryseobacterium carnipullorum DSM 25581T (98.7%) and Chryseobacterium oncorhychi 701B-08T (98%). The genome is 4,910,468 bp long with 73 scaffolds and 4300 protein-coding genes. The anti-SMASH analysis of whole genome showed ten putative biosynthetic gene clusters responsible for various secondary metabolites. The sole respiratory quinone is MK-6. The major cellular fatty acids are iso-C15:0, iso-C17:1 ω9c, iso-C17:0 3-OH, summed feature 3 (iso-C15 :0 2-OH/C16 :1ω7c) and anteiso-C15:0. The major polar lipid is phosphatidylethanolamine. The DNA G + C content of the type strain is 36.9 mol%. In addition, the average nucleotide identity and in silico DNA-DNA hybridization  relatedness values between strain RP-3-3T and phylogenetically closest members are below the threshold value for species delineation. Based on genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain RP-3-3T represents novel species in the genus Chryseobacterium, for which the name Chryseobacterium antibioticum sp. nov. is proposed. The type strain is RP-3-3T (=KACC 21620T = NBRC 114360T).

Genome-enabled discovery of anthraquinone biosynthesis in Senna tora.

Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.

The genome insights of Streptomyces lannensis T1317-0309 reveals actinomycin D production.

The members of Streptomyces have been identified as a major source of antimicrobial agents with broad spectrum. This study is mainly focused on bioactivity-guided isolation and characterization of bioactive molecule from strain Streptomyces sp. T1317-0309 and its whole-genome sequence analysis for possible isolation of novel natural products. Strain Streptomyces sp. T1317-0309 showed 100% sequence similarity with strain Streptomyces lannensis TA4-8T consisting 10, 453,255 bp of genome with 5 scaffolds and 69.9 mol% G + C content. The genome analyses revealed a total of 17 putative biosynthetic gene clusters (BGCs) responsible for various secondary metabolites including actinomycin, bacteriocin, ectoine, melanin, terpene, siderophore, betalactone, NRPS, T2PKS, and T3PKS. The BGC and bioactivity-guided purification of ethyl acetate extract of strain T1317-0309 showed the great potency of antimicrobial activities against various gram-positive multi-drug resistant human pathogens including MRSA. The BGC-predicted bioactive secondary metabolite was identified by various NMR analyses and confirmed as actinomycin D. In addition, this study reveals the first genome study of Streptomyces lannensis as a novel source for actinomycin D.

Regio-specific biotransformation of alizarin to alizarin methoxide with enhanced cytotoxicity against proliferative cells.

Alizarin has been reported to have an antigenotoxic activity along with an inhibitory effect on the tumor cell growth of human colon carcinoma cells. Alizarin was biotransformed into an O-methoxide derivative using O-methyltransferase from Streptomyces avermitilis MA4680 (SaOMT2) to enhance its bioefficacy. The biotransformed product was extracted, purified, and characterized using various chromatographic and spectroscopic analyses, and confirmed to be an alizarin 2-O-methoxide. The antiproliferative activity of the compound against gastric cancer cells (AGS), uterine cervical cancer (Hela), liver cancer (HepG2), and normal cell lines was investigated. Alizarin 2-O-methoxide showed an inhibitory effect on all three cancer-cell lines at very low concentrations, from 0.078 µM, with no cytotoxicity against 267B1 (human prostate epithelial) and MRC-5 (normal human fetal lung fibroblast).

Exploring the Nucleophilic N- and S-Glycosylation Capacity of Bacillus licheniformis YjiC Enzyme.

YjiC, a glycosyltransferase from Bacillus licheniformis, is a well-known versatile enzyme for glycosylation of diverse substrates. Although a number of O-glycosylated products have been produced using YjiC, no report has been updated for nucleophilic N-, S-, and C- glycosylation. Here, we report the additional functional capacity of YjiC for nucleophilic N- and S- glycosylation using a broad substrate spectrum including UDP-α-D-glucose, UDP-N-acetyl glucosamine, UDP-N-acetylgalactosamine, UDP-α-D-glucuronic acid, TDP-α-L-rhamnose, TDP-α-D-viosamine, and GDP-α-Lfucose as donor and various amine and thiol groups containing natural products as acceptor substrates. The results revealed YjiC as a promiscuous enzyme for conjugating diverse sugars at amine and thiol functional groups of small molecules applicable for generating glycofunctionalized chemical diversity libraries. The glycosylated products were analyzed using HPLC and LC/MS and compared with previous reports.

Characterization of Tailoring Steps of Nargenicin A1 Biosynthesis Reveals a Novel Analogue with Anticancer Activities.

Nargenicin A1(1) is an antibacterial macrolide with effective activity against various Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. Due to the promising properties of this compound in inhibiting cell proliferation, immunomodulation, and the cell protective effect, there has been significant interest in this molecule. Recently, the biosynthetic gene cluster (BGC) of 1 was reported from Nocardia argentinesis and Nocardia arthritidis. In addition, two crucial enzymes involved in the formation of the core decalin moiety and postmodification of the decalin moiety by an ether bridge were characterized. This study reports on the BGC of 1 from Nocardia sp. CS682. In addition, the direct capture and heterologous expression of nar BGC from Nocardia sp. CS682 in Streptomyces venezuelae led to the production of 1. Further metabolic profiling of wild type, Nocardia sp. CS682 in optimized media (DD media) resulted in the isolation of two acetylated derivatives, 18-O-acetyl-nodusmicin and 18-O-acetyl-nargenicin. The post-PKS modification pathway in biosynthesis of 1 was also deciphered by identifying intermediates and/or in vitro enzymatic reactions of NgnP1, NgnM, and NgnO3. Different novel analogues of 1, such as compound 6, compound 7, 23-demethyl 8,13-deoxy-nodusmicin (8), 23-demethyl 8,13-deoxynargenicin (9), 8,13-deoxynodusmicin (10), and 8,13-deoxynargenicin (11), were also characterized, which extended our understanding of key post-PKS modification steps during the biosynthesis of 1. In addition, the antimicrobial and anticancer activities of selected analogues were also evaluated, whereas compound 9 was shown to exhibit potent antitumor activity by induction of G2/M cell cycle arrest, apoptosis, and autophagy.

Biosynthesis of Rhamnosylated Anthraquinones in Escherichia coli.

Rhamnose is a naturally occurring deoxysugar present as a glycogenic component of plant and microbial natural products. A recombinant mutant Escherichia coli strain was developed by overexpressing genes involved in the TDP-L-rhamnose biosynthesis pathway of different bacterial strains and Saccharothrix espanaensis rhamnosyl transferase to conjugate intrinsic cytosolic TDP-L-rhamnose with anthraquinones supplemented exogenously. Among the five anthraquinones (alizarin, emodin, chrysazin, anthrarufin, and quinizarin) tested, quinizarin was biotransformed into a rhamoside derivative with the highest conversion ratio by whole cells of engineered E. coli. The quinizarin glycoside was identified by various chromatographic and spectroscopic analyses. The anti-proliferative property of the newly synthesized rhamnoside, quinizarin-4-O-α-L-rhamnoside, was assayed in various cancer cells.

Increased Production of Dicinnamoylmethane Via Improving Cellular Malonyl-CoA Level by Using a CRISPRi in Escherichia coli.

Curcuminoids are natural phenylpropanoids that are biosynthesized via an L-phenylalanine metabolism pathway in turmeric (Curcuma longa L.). Curcuminoids have various chemopreventive activities and pharmaceutical applications in human life. In this study, we synthesized dicinnamoylmethane, one principal component of curcuminoids, from cinnamic acid by means of co-expression of Oryza sativa curcuminoid synthase and Petroselinum crispum 4-coumarate-CoA ligase in Escherichia coli BL21 (DE3). Moreover, we used CRISPRi systems to knock down the genes in a tricarboxylic acid cycle and fatty acid biosynthesis pathway. The repression of target genes led to an increase of up to 0.236 µmol g-1 DCW of malonyl-CoA in cytosol-engineered E. coli and subsequently increased the biosynthesis of dicinnamoylmethane. We found that the S10 strain containing a CRISPRi repression for three genes, fabF, fabD, and mdh, showed the highest amount of dicinnamoylmethane of 7.54 µM, which is 5.76-fold higher than that of the wild-type strain. Finally, 41.94 µM (~ 11.6 mg) of dicinnamoylmethane was obtained in a 3-L fermenter.

Two Trifunctional Leloir Glycosyltransferases as Biocatalysts for Natural Products Glycodiversification.

Two promiscuous Bacillus licheniformis glycosyltransferases, YdhE and YojK, exhibited prominent stereospecific but nonregiospecific glycosylation activity of 20 different classes of 59 structurally different natural and non-natural products. Both enzymes transferred various sugars at three nucleophilic groups (OH, NH2, SH) of diverse compounds to produce O-, N-, and S-glycosides. The enzymes also displayed a catalytic reversibility potential for a one-pot transglycosylation, thus bestowing a cost-effective application in biosynthesis of glycodiversified natural products in drug discovery.

Engineering actinomycetes for biosynthesis of macrolactone polyketides.

Actinobacteria are characterized as the most prominent producer of natural products (NPs) with pharmaceutical importance. The production of NPs from these actinobacteria is associated with particular biosynthetic gene clusters (BGCs) in these microorganisms. The majority of these BGCs include polyketide synthase (PKS) or non-ribosomal peptide synthase (NRPS) or a combination of both PKS and NRPS. Macrolides compounds contain a core macro-lactone ring (aglycone) decorated with diverse functional groups in their chemical structures. The aglycon is generated by megaenzyme polyketide synthases (PKSs) from diverse acyl-CoA as precursor substrates. Further, post-PKS enzymes are responsible for allocating the structural diversity and functional characteristics for their biological activities. Macrolides are biologically important for their uses in therapeutics as antibiotics, anti-tumor agents, immunosuppressants, anti-parasites and many more. Thus, precise genetic/metabolic engineering of actinobacteria along with the application of various chemical/biological approaches have made it plausible for production of macrolides in industrial scale or generation of their novel derivatives with more effective biological properties. In this review, we have discussed versatile approaches for generating a wide range of macrolide structures by engineering the PKS and post-PKS cascades at either enzyme or cellular level in actinobacteria species, either the native or heterologous producer strains.

Correction to: Cascade biocatalysis systems for bioactive naringenin glucosides and quercetin rhamnoside production from sucrose.

The name of the author "Yamaguchi Tokutaro" is incorrect for the first and last name has been interchanged. The correct presentation is "Tokutaro Yamaguchi".

Biocatalytic Synthesis of Non-Natural Monoterpene O-Glycosides Exhibiting Superior Antibacterial and Antinematodal Properties.

A promiscuous Bacillus glycosyltransferase (YjiC) was explored for the enzymatic synthesis of monoterpene O-glycosides in vitro and in vivo. YjiC converted seven monoterpenes into 41 different sugar-conjugated novel glycoside derivatives. The whole-cell biotransformation of the same set of monoterpenes exhibited robust enzyme activity to synthesize O-glucosyl derivatives from Escherichia coli. These newly synthesized selected monoterpene-O-glucosyl derivatives exhibited enhanced antibacterial activities against human pathogenic bacteria and antinematodal activities against pine wood nematode Bursaphelenchus xylophilus.

Cascade biocatalysis systems for bioactive naringenin glucosides and quercetin rhamnoside production from sucrose.

Two sustainable and cost-effective cascade enzymatic systems were developed to regenerate uridine diphosphate (UDP)-α-D-glucose and UDP-ß-L-rhamnose from sucrose. The systems were coupled with the UDP generating glycosylation reactions of UDP sugar-dependent glycosyltransferase (UGT) enzymes mediated reactions. As a result, the UDP generated as a by-product of the GT-mediated reactions was recycled. In the first system, YjiC, a UGT from Bacillus licheniformis DSM 13, was used for transferring glucose from UDP-α-D-glucose to naringenin, in which AtSUS1 from Arabidopsis thaliana was used to synthesize UDP-α-D-glucose and fructose as a by-product from sucrose. In the second system, flavonol 7-O-rhamnosyltransferase (AtUGT89C1) from A. thaliana was used to transfer rhamnose from UDP-ß-L-rhamnose to quercetin, in which AtSUS1 along with UDP-ß-L-rhamnose synthase (AtRHM1), also from A. thaliana, were used to produce UDP-ß-L-rhamnose from the same starter sucrose. The established UDP recycling system for the production of naringenin glucosides was engineered and optimized for several reaction parameters that included temperature, metal ions, NDPs, pH, substrate ratio, and enzymes ratio, to develop a highly feasible system for large-scale production of different derivatives of naringenin and other natural products glucosides, using inexpensive starting materials. The developed system showed the conversion of about 37 mM of naringenin into three different glucosides, namely naringenin, 7-O-ß-D-glucoside, naringenin, 4'-O-ß-D-glucoside, and naringenin, 4',7-O-ß-D-diglucoside. The UDP recycling (RCmax) was 20.10 for naringenin glucosides. Similarly, the conversion of quercetin to quercetin 7-O-α-L-rhamnoside reached a RCmax value of 10.0.

Biotechnological Advances in Resveratrol Production and its Chemical Diversity.

The very well-known bioactive natural product, resveratrol (3,5,4'-trihydroxystilbene), is a highly studied secondary metabolite produced by several plants, particularly grapes, passion fruit, white tea, and berries. It is in high demand not only because of its wide range of biological activities against various kinds of cardiovascular and nerve-related diseases, but also as important ingredients in pharmaceuticals and nutritional supplements. Due to its very low content in plants, multi-step isolation and purification processes, and environmental and chemical hazards issues, resveratrol extraction from plants is difficult, time consuming, impracticable, and unsustainable. Therefore, microbial hosts, such as Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum, are commonly used as an alternative production source by improvising resveratrol biosynthetic genes in them. The biosynthesis genes are rewired applying combinatorial biosynthetic systems, including metabolic engineering and synthetic biology, while optimizing the various production processes. The native biosynthesis of resveratrol is not present in microbes, which are easy to manipulate genetically, so the use of microbial hosts is increasing these days. This review will mainly focus on the recent biotechnological advances for the production of resveratrol, including the various strategies used to produce its chemically diverse derivatives.

Biosynthesis of resveratrol and piceatannol in engineered microbial strains: achievements and perspectives.

Resveratrol (3,5,4'-trihydroxystilbene) and piceatannol (3,5,3',4'-tetrahydroxystilbene) are well-known natural products that are produced by plants. They are important ingredients in pharmaceutical industries and nutritional supplements. They display a wide spectrum of biological activity. Thus, the needs for these compounds are increasing. The natural products have been found in diverse plants, mostly such as grapes, passion fruit, white tea, berries, and many more. The extraction of these products from plants is quite impractical because of the low production in plants, downstream processing difficulties, chemical hazards, and environmental issues. Thus, alternative production in microbial hosts has been devised with combinatorial biosynthetic systems, including metabolic engineering, synthetic biology, and optimization in production process. Since the biosynthesis is not native in microbial hosts such as Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum, genetic engineering and manipulation have made it possible. In this review, the discussion will mainly focus on recent progress in production of resveratrol and piceatannol, including the various strategies used for their production.