A large conserved family of small-molecule carboxyl methyltransferases identified from microorganisms

Efficient Synthesis of Steroidal Intermediates with a C17 Side Chain from Phytosterols by Genetically Modified Mycolicibacterium neoaurum NRRL B-3805 Strain

22-Hydroxy-23,24-bisnorchol-4-ene-3-one (4-HBC) and 3-oxo-4,17-pregnadiene-20-carboxylic acid methyl ester (PDCE) are useful precursors for the synthesis of steroidal active pharmaceutical ingredients. In this study, we identify the sterol metabolism-related genes, which encode the aldolases (Ltp2 and Thl) and carboxylic acid reductases (CAR) in Mycolicibacterium neoaurum NRRL B-3805 (B3805), by analysis of the metabolites from phytosterols biotransformation. Based on these results, a genetically modified strain is constructed by disrupting the kstD, ltp2, and hsd4A genes and overexpressing the aldolase gene (thl) in the strain B3805. This recombinant strain (B3805V) is able to transform 5 g L-1 phytosterols to 2.0 g L-1 4-HBC without detectable AD by-product. Additionally, by disrupting the ltp2 and car genes, a strain (strain B3805VI) is obtained to transform phytosterols to PDCE with 1.44 g L-1 titer. The PDCE concentration is further increased by about 42% to 2.1 g L-1 without 4-HBC by-product by deleting thl gene (strain B3805VII). On the preparative scale, the strain B3805VII transforms 10 g L-1 of phytosterols into PDCE with 5.1 g L-1. This study presents one-step bioproduction of pharmaceutically important 4-HBC and PDCE with high yield and purity from bio-renewable phytosterols, which are readily available as a by-product from the plant oil industry.

Ferulic acid production in Escherichia coli by engineering caffeic acid O-methyltransferase

Methylation is a key step for the structure diversification of natural products, however, the low activity and substrate promiscuity of methyltransferase remain challenges for efficient biosynthesis. In this study, taking the synthesis of ferulic acid as a case, we attempted to improve the catalytic efficiency of caffeic acid O-methyltransferase (AtCOMT) by engineering its binding pocket and interactions with substrate. Through reshaping the substrate binding pocket and increasing the hydrogen bond network, L125R/I317E mutant with highly catalytic efficiency and substrate specificity was obtained. Compared with the wild-type AtCOMT, the kcat/Km increased by 5.79-fold. Molecular dynamics simulation verified that the increased activity and specificity of AtCOMT were derived from the tighter substrate binding pocket and stronger enzyme-substrate interactions produced by the designed hydrogen bonds and salt bridges. Eventually, 1.273 g/L ferulic acid was obtained by fed-batch fermentation, which was 21.3-fold compared with the WT. This work provided the foundation for efficient synthesis of ferulic acid by AtCOMT, and also illustrated that rational design of substrate binding pocket and hydrogen bond network would be an effective strategy for improving the activity and substrate specificity of enzyme.

Cloning and bioinformatics analysis of key gene ShOMT3 of podophyllotoxin biosynthesis pathway in Sinopodophyllum hexandrum

Sinopodophyllum hexandrum (S. hexandrum) is an endangered traditional Chinese medicine as abundant podophyllotoxin with powerful anticancer activity. In this study, the rootstalks of S. hexandrum from different geographical locations in China [S1 (Gansu) and S2 (Shaanxi)] were used as research materials to clone the key gene pluviatolide O-methyltransferase 3 (ShOMT3) in the podophyllotoxin biosynthetic pathway. Subsequently, bioinformatics analysis of the ShOMT3 gene and its encoded protein was subjected to bioinformatics analysis using various analysis software including ProtParam, DeepTMHMM, SubLoc, Signal-P 5.0, and Swiss-model. The results of the analysis revealed that the CDS region of the ShOMT3 gene is 1119 bp long, encoding 372 amino acids. The theoretical molecular weight of the ShOMT3 protein is 41.32784 kD, and the theoretical isoelectric point (pI) is 5.27. The instability coefficient of the protein is 46.05, the aliphatic index is 93.58, and the grand average of hydropathicity (GRAVY) is 0.037, indicating that it is an unstable hydrophobic protein. The protein does not contain transmembrane domains or signal peptides, indicating that it is a non-secreted protein. Secondary structure prediction results suggests that the protein consists of alpha helices, random coils, extended strands, and beta-turns. Tertiary structure prediction results suggests that the protein functions as a monomer. In the phylogenetic tree, the ShOMT3 protein has the highest homology with Podophyllum peltatum (P. peltatum). The successful cloning and bioinformatics analysis of the ShOMT3 gene provide theoretical basis and excellent genetic resources for the molecular regulatory mechanism analysis of the podophyllotoxin biosynthetic pathway and molecular breeding in S. hexandrum.

A metabologenomics strategy for rapid discovery of polyketides derived from modular polyketide synthases

Bioinformatics-guided metabolomics is a powerful means for the discovery of novel natural products. However, the application of such metabologenomics approaches on microbial polyketides, a prominent class of natural products with diverse bioactivities, remains largely hindered due to our limited understanding on the mass spectrometry behaviors of these metabolites. Here, we present a metabologenomics approach for the targeted discovery of polyketides biosynthesized by modular type I polyketide synthases. We developed the NegMDF workflow, which uses mass defect filtering (MDF) supported by bioinformatic structural prediction, to connect the biosynthetic gene clusters to corresponding metabolite ions obtained under negative ionization mode. The efficiency of the NegMDF workflow is illustrated by rapid characterization of 22 polyketides synthesized by three gene clusters from a well-characterized strain Streptomyces cattleya NRRL 8057, including cattleyatetronates, new members of polyketides containing a rare tetronate moiety. Our results showcase the effectiveness of the MDF-based metabologenomics workflow for analyzing microbial natural products, and will accelerate the genome mining of microbial polyketides.

A Bifunctional Methyltransferase in Biosynthesis of Antitumor Antibiotic Streptonigrin

Streptonigrin (STN, 1) is a highly functionalized aminoquinone alkaloid antibiotic with broad and potent antitumor activity. STN structurally contains four methyl groups belonging to two types: C-methyl group and O-methyl groups. Here, we report the biochemical characterization of the O-methyltransferase StnQ2 that can catalyze both the methylation of a hydroxyl group and a carboxyl group in the biosynthesis of streptonigrin. This work not only provides a new insight into methyltransferases, but also advances the elucidation of the complete biosynthetic pathway of streptonigrin.

Structural basis for substrate flexibility of the O-methyltransferase MpaG' involved in mycophenolic acid biosynthesis

MpaG' is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase involved in the compartmentalized biosynthesis of mycophenolic acid (MPA), a first-line immunosuppressive drug for organ transplantations and autoimmune diseases. MpaG' catalyzes the 5-O-methylation of three precursors in MPA biosynthesis including demethylmycophenolic acid (DMMPA), 4-farnesyl-3,5-dihydroxy-6-methylphthalide (FDHMP), and an intermediate containing three fewer carbon atoms compared to FDHMP (FDHMP-3C) with different catalytic efficiencies. Here, we report the crystal structures of S-adenosyl-L-homocysteine (SAH)/DMMPA-bound MpaG', SAH/FDHMP-3C-bound MpaG', and SAH/FDHMP-bound MpaG' to understand the catalytic mechanism of MpaG' and structural basis for its substrate flexibility. Structural and biochemical analyses reveal that MpaG' utilizes the catalytic dyad H306-E362 to deprotonate the C5 hydroxyl group of the substrates for the following methylation. The three substrates with differently modified farnesyl moieties are well accommodated in a large semi-open substrate binding pocket with the orientation of their phthalide moiety almost identical. Based on the structure-directed mutagenesis, a single mutant MpaG'Q267A is engineered with significantly improved catalytic efficiency for all three substrates. This study expands the mechanistic understanding and the pocket engineering strategy for O-methyltransferases involved in fungal natural product biosynthesis. Our research also highlights the potential of O-methyltransferases to modify diverse substrates by protein design and engineering.

Recent developments in the enzymatic modifications of steroid scaffolds

Steroids are an important family of bioactive compounds. Steroid drugs are renowned for their multifaceted pharmacological activities and are the second-largest category in the global pharmaceutical market. Recent developments in biocatalysis and biosynthesis have led to the increased use of enzymes to enhance the selectivity, efficiency, and sustainability for diverse modifications of steroids. This review discusses the advancements achieved over the past five years in the enzymatic modifications of steroid scaffolds, focusing on enzymatic hydroxylation, reduction, dehydrogenation, cascade reactions, and other modifications for future research on the synthesis of novel steroid compounds and related drugs, and new therapeutic possibilities.