Engineering the Entrance of a Flavonoid Glycosyltransferase Promotes the Glycosylation of Etoposide Aglycone.

Enzyme entrances, which function as the first molecular filters, influence substrate selectivity and enzymatic activity. Because of low binding affinities, engineering enzyme entrances that recognize non-natural substrates is a major challenge for artificial biocatalyst design. Here, the entrance of flavonoid glycosyltransferase UGT78D2 was engineered to promote the recognition of the aglycone of etoposide, a chemotherapeutic agent. We found that Q258, S446, R444, and R450, the key residues surrounding the substrate entrance, specifically guide the flux of etoposide aglycone, which has a high steric hindrance, into the active site; this activity was inferred to be determined by the entrance size and hydrophobic and electrostatic interactions. Engineering the coordination of Q258 and S446 to increase the entrance size and hydrophobic interaction between UGT78D2 and etoposide aglycone increased the affinity by 10.10-fold and the conversion by 10%. The entrance-engineering strategy applied in this study can improve the design of artificial biocatalysts.

The Advances and Challenges in Enzymatic C-glycosylation of Flavonoids in Plants.

Flavonoid glycosides play determinant roles in plants and have considerable potential for applications in medicine and biotechnology. Glycosyltransferases transfer a sugar moiety from uridine diphosphateactivated sugar molecules to an acceptor flavonoid via C-O and C-C linkages. Compared with O-glycosyl flavonoids, C-glycosyl flavonoids are more stable, resistant to glycosidase or acid hydrolysis, exhibit better pharmacological properties, and have received more attention. In this study, we discuss the mining of C-glycosyl flavones and the corresponding C-glycosyltransferases and evaluate the differences in structure and catalytic mechanisms between C-glycosyltransferase and O-glycosyltransferase. We conclude that promiscuity and specificity are key determinants for general flavonoid C-glycosyltransferase engineering and summarize the C-glycosyltransferase engineering strategy. A thorough understanding of the properties, catalytic mechanisms, and engineering of C-glycosyltransferases will be critical for future biotechnological applications in areas such as the production of desired C-glycosyl flavonoids for nutritional or medicinal use.

YALI0C22088g from Yarrowia lipolytica catalyses the conversion of l-methionine into volatile organic sulfur-containing compounds.

The enzymatic conversion of l-methionine (l-Met) into volatile organic sulfur-containing compounds (VOSCs) plays an important role in developing the characteristic aroma of foods. However, the mechanism for the direct conversion of l-Met into VOSCs is still unclear in yeast cells used to make food products. Here, we show that the transcription profile of YALI0C22088g from Yarrowia lipolytica correlates positively with l-Met addition. YALI0C22088g catalyses the γ-elimination of l-Met, directly converting l-Met into VOSCs. YALI0C22088g also exhibits strong C-S lysis activities towards l-cystathionine and the other sulfur-containing compounds and forms a distinct cystathionine-γ-lyase subgroup. We identified eight key amino acid residues in YALI0C22088g, and we inferred that the size of the tunnel and the charges carried by the entrance amino acid residue are the determinants for the enzymatic conversion of l-Met into VOSCs. These findings reveal the formation mechanism of VOSCs produced directly from l-Met via the demethiolation pathway in Yarrowia lipolytica, which provides a rationale for engineering the enzymatic conversion of l-Met into VOSCs and thus stimulates the enzymatic production of aroma compounds.

Enzymatic O-Glycosylation of Etoposide Aglycone by Exploration of the Substrate Promiscuity for Glycosyltransferases.

The 4-O-ß-d-glucopyranoside of DMEP ((-)-4'-desmethylepipodophyllotoxin) (GDMEP), a natural product from Podophyllum hexandrum, is the direct precursor to the topoisomerase inhibitor etoposide, used in dozens of chemotherapy regimens for various malignancies. The biosynthesis pathway for DMEP has been completed, while the enzyme for biosynthesizing GDMEP is still unclear. Here, we report the enzymatic O-glycosylation of DMEP with 53% conversion by exploring the substrate promiscuity and entrances of glycosyltransferases. Notably, we found 6 essential amino acid residues surrounding the putative substrate entrances exposed to the protein surface in UGT78D2, CsUGT78D2, and CsUGT78D2-like, and these residues may determine substrate specificity and high O-glycosylation activity toward DMEP. Our results provide an effective route for one-step synthesis of GDMEP. Identification of the key residues and entrances of glycosyltransferases will promote precise identification of glycosyltransferase biocatalysts for novel substrates and provide a rational basis for glycosyltransferase engineering.

Regulatory Networks Governing Methionine Catabolism into Volatile Organic Sulfur-Containing Compounds in Clonostachys rosea.

Adaptation to environmental perturbations requires living systems to coordinately regulate signaling pathways, gene expression, and metabolism. To better understand the mechanisms underlying adaptation, the regulatory nodes within networks must be elucidated. Here, ARO8-2 (which encodes an aminotransferase), PDC (which encodes a decarboxylase), and STR3 (which encodes a demethiolase) were identified as key genes involved in the catabolism of methionine in the mycoparasitic fungus Clonostachys rosea, isolated from Tuber melanosporum ascocarps. Exogenous Met induced the transcription of ARO8-2 and PDC but repressed the transcription of STR3, which is controlled by the putative MSN2 and GLN3 binding sites responding to nitrogen catabolite repression. Met and its structural derivatives function as glutamine synthetase inhibitors, resulting in the downregulation of STR3 expression. The putative GLN3 binding site was necessary for STR3 downregulation. In Saccharomyces cerevisiae, Met and its structural derivatives also triggered downregulation of demethiolase gene expression. Altogether, the results indicated that exogenous Met triggered nitrogen catabolite repression, which stimulated the Ehrlich pathway and negatively regulated the demethiolation pathway via the methionine sulfoximine-responsive regulatory pathway. This finding revealed the regulatory nodes within the networks controlling the catabolism of Met into volatile organic sulfur-containing compounds, thereby enhancing our understanding of adaptation.IMPORTANCE Methionine shuttles organic nitrogen and plays a central role in nitrogen metabolism. Exogenous Met strongly induces the expression of ARO8-2 and PDC, represses the expression of STR3, and generates volatile organic sulfur-containing compounds via the Ehrlich and demethiolation pathways. In this study, we used genetic, bioinformatic, and metabolite-based analyses to confirm that transcriptional control of the aminotransferase gene ARO8-2, the decarboxylase gene PDC, and the demethiolase gene STR3 modulates Met catabolism into volatile organic sulfur-containing compounds. Importantly, we found that, in addition to the Ehrlich pathway, the demethiolation pathway was regulated by a nitrogen catabolite repression-sensitive regulatory pathway that controlled the transcription of genes required to catabolize poor nitrogen sources. This work significantly advances our understanding of nitrogen catabolite repression-sensitive transcriptional regulation of sulfur-containing amino acid catabolism and provides a basis for engineering Met catabolism pathways for the production of fuel and valuable flavor alcohols.

Regulating ehrlich and demethiolation pathways for alcohols production by the expression of ubiquitin-protein ligase gene HUWE1.

Ehrlich and demethiolation pathways as two competing branches converted amino acid into alcohols. Controlling both pathways offers considerable potential for industrial applications including alcohols overproduction, flavor-quality control and developing new flavors. While how to regulate ehrlich and demethiolation pathways is still not applicable. Taking the conversion of methionine into methionol and methanethiol for example, we constructed two suppression subtractive cDNA libraries of Clonostachys rosea by using suppression subtractive hybridization (SSH) technology for screening regulators controlling the conversion. E3 ubiquitin-protein ligase gene HUWE1 screened from forward SSH library was validated to be related with the biosynthesis of end products. Overexpressing HUWE1 in C. rosea and S. cerevisiae significantly increased the biosynthesis of methanethiol and its derivatives in demethiolation pathway, while suppressed the biosynthesis of methional and methionol in ehrlich pathway. These results attained the directional regulation of both pathways by overexpressing HUWE1. Thus, HUWE1 has potential to be a key target for controlling and enhancing alcohols production by metabolic engineering.

Clonostachys rosea demethiolase STR3 controls the conversion of methionine into methanethiol.

Eukaryote-derived methioninase, catalyzing the one-step degradation of methionine (Met) to methanethiol (MTL), has received much attention for its low immunogenic potential and use as a therapeutic agent against Met-dependent tumors. Although biological and chemical degradation pathways for Met-MTL conversion are proposed, the concrete molecular mechanism for Met-MTL conversion in eukaryotes is still unclear. Previous studies demonstrated that α-keto-methylthiobutyric acid (KMBA), the intermediate for Met-MTL conversion, was located extracellularly and the demethiolase STR3 possessed no activities towards Met, which rule out the possibility of intracellular Met-MTL conversion pathway inside eukaryotes. We report here that degradation of Met resulted in intracellular accumulation of KMBA in Clonostachys rosea. Addition of Met to culture media led to the production of MTL and downregulation of STR3, while incubation of Met with surrogate substrate α-ketoglutaric acid enhanced the synthesis of MTL and triggered the upregulation of STR3. Subsequent biochemical analysis with recombinant STR3 showed that STR3 directly converted both Met and its transamination product KMBA to MTL. These results indicated that STR3 as rate-limiting enzyme degrades Met and KMBA into MTL. Our findings suggest STR3 is a potential target for therapeutic agents against Met-dependent tumors and aging.

[Isolation of a monocrotophos-degrading bacterial strain and characterization of enzymatic degradation].

A monocrotophos [dimethyl (E)-1-2-methylcarbamoylvinylphosphate or MCP] -degrading strain named as M-1 was isolated from sludge collected from the wastewater treatment pool of a pesticide factory and identified as Paracoccus sp. according to its morphology and biochemical properties and 16S rDNA sequence analysis. Using MCP as a sole carbon source, M-1 was able to degrade MCP(100 mg x L(-1)) by 92.47% in 24 h. The key enzyme(s) involved in the initial biodegradation of monocrotophos in M-1 was shown to be constitutively expressed cytosolic proteins and showed the greatest activity at pH 8.0 and 25 degrees C, with its Michaelis-Mentn's constant (K(m)) and maximum degradation rate (V(max)) of 0.29 micromol x mL(-1) and 682.12 micromol (min x mg)(-1) respectively. This degrading enzyme(s) was sensitive to high temperature, but kept high activity under alkaline conditions.

[Construction of a versatile degrading bacteria Pseudomonas putida KT2440-DOP and its degrading characteristics].

Triazophos is a kind of organophosphorous pesticide which was widely used by farmers all over the world in 1990's. It is effective in controlling pesticide but harmful to human beings. Bioremediation is an effective and economic method to treat environment that has been polluted by hazardous organic compounds, so researchers paid much attention in this area. Most of which focused on isolating functional bacteria, studying its degrading mechanism, and cloning degradation-related genes. MP-4 was isolated from soil polluted by Triazophos for a long time and identified as Ochrobactrum sp.. The triazophos hydrolase (tpd) gene was cloned by the method of shotgun cloning, and the sequences were determined and analyzed. In the former tests it was found that there was only 18 base pairs different in tpd gene from mpd gene, which was isolated from methyl parathion degrading strain Pseudomonas putida DLL-1. Enzyme TPD can hydrolyze triazophos and methyl parathion while MPD cannot hydrolyze triazophos. Pseudomonas putida KT2440 is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. This bacterium is known for its diverse metabolism and potential for development of biopesticides and plant growth promoters because of its ability to colonize rhizosphere of crop plants. Tpd gene was isolated from the genomic DNA of Ochrobactrum sp. MP-4 by PCR amplification. Recombinant plasmids pTPD was constructed by ligating tpd gene into broad host vector pBBRMCS-5. With the help of plasmid pRK2013, pTPD was transferred into Pseudomonas putida KT2440 to construct KT2440-DOP. KT2440-DOP can degrade many organophosphate pesticides and aromatics compounds. The specific activity of organophosphate hydrolase of KT2440-DOP was approximately 2 times of MP-4. Later, parameters affecting bioremediation of Organophosphate pesticide in soil using KT2440-DOP will be studied.

Isolation and characterization of a denitrifying monocrotophos-degrading Paracoccus sp. M-1.

A bacterium strain, which is capable of degrading monocrotophos, was isolated from sludge collected from the bottom of a wastewater treatment system of a chemical factory, and named M-1. On the basis of the results of the cellular morphology, physiological and chemotaxonomic characteristics and phylogenetic similarity of 16S rDNA gene sequences, the strain was identified as a Paracoccus sp. The ability of the strain to mineralize monocrotophos was investigated under different culture conditions. Other organophosphorus insecticides and amide herbicides were also degraded by M-1. The key enzyme (s) involved in the initial biodegradation of monocrotophos in M-1 was shown to be a constitutively expressed cytosolic protein. The addition of M-1 (10(6) CFU g(-1)) to fluvo-aquic soil and a high-sand soil containing monocrotophos (50 mg kg(-1)) resulted in a higher degradation rate than that obtained from noninoculated soil. This microbial culture has great potential utility for the bioremediation of wastewater or soil contaminated with organophosphorus pesticides and amide herbicides.

[Glycine betaine supplied exogenously enhance salinity tolerance of Pseudomonas putida DLL-1].

The salinity tolerance characteristic of Pseudomonas putida DLL-1 and the environmental factors affecting the salinity tolerance of DLL-1 were investigated. The result showed that the enrichment of culture medium influenced the salt tolerance of DLL-1, in complete medium DLL-1 could survive higher salinities than in chemically defined medium. When inoculated to complete medium with 1mol/L NaCl, the least initial biomass guarantee DLL-1 surviving was 1/100(V/V) of the medium volumes. But when inoculated to chemically defined medium with 1mol/L NaCl, the least initial biomass guarantee DLL-1 surviving was 1/10(V/V) of the medium volumes. The effects of glycine betaine exogenously supplied on the salinity tolerance of DLL-1 and its osmo protection mechanisms were also studied. The results indicated that the glycine betaine present externally could promote the growth of DLL-1 under high salinity. 10mg/L of exogenous glycine betaine was sufficient to promote the growth condition of DLL-1 cells under high salinities. 150mg/L glycine betaine could support DLL-1 cells grow in chemically defined medium with 1.2mol/L NaCl. The presence of glycine betaine in chemically defined medium could reduce significantly the lag time and generation time and increase the final biomass of DLL-1 under salt stress. Compared with the control without exogenous glycine betaine, the lag time of the treatment with exogenous glycine betaine could be reduced from 24h to 6h, and the generation time from 60min to 35.7min, the final OD610 value of culture increased from 1.29 to 1.57. Under osmotic stress, DLL-1 cells could synthesis glycine betaine, trehalose and free amino acid as the main compatible solute. When exogenously supplied, DLL-1 cells accumulated exogenous glycine betaine rapidly from medium to balance the extracellular osmolality instead of the synthesis of compatible solutes.