Identification of genes involved in shea butter biosynthesis from Vitellaria paradoxa fruits through transcriptomics and functional heterologous expression

Advancing Insights into Probiotics during Vegetable Fermentation

Fermented vegetables have a long history and are enjoyed worldwide for their unique flavors and health benefits. The process of fermentation improves the nutritional value, taste, and shelf life of foods. Microorganisms play a crucial role in this process through the production of metabolites. The flavors of fermented vegetables are closely related to the evaluation and succession of microbiota. Lactic acid bacteria (LABs) are typically the dominant bacteria in fermented vegetables, and they help inhibit the growth of spoilage bacteria and maintain a healthy gut microbiota in humans. However, homemade and small-scale artisanal products rely on spontaneous fermentation using bacteria naturally present on fresh vegetables or from aged brine, which may introduce external microorganisms and lead to spoilage and substandard products. Hence, understanding the role of LABs and other probiotics in maintaining the quality and safety of fermented vegetables is essential. Additionally, selecting probiotic fermentation microbiota and isolating beneficial probiotics from fermented vegetables can facilitate the use of safe and healthy starter cultures for large-scale industrial production. This review provides insights into the traditional fermentation process of making fermented vegetables, explains the mechanisms involved, and discusses the use of modern microbiome technologies to regulate fermentation microorganisms and create probiotic fermentation microbiota for the production of highly effective, wholesome, safe, and healthy fermented vegetable foods.

Research advances in probiotic fermentation of Chinese herbal medicines

Chinese herbal medicines (CHM) have been used to cure diseases for thousands of years. However, the bioactive ingredients of CHM are complex, and some CHM natural products cannot be directly absorbed by humans and animals. Moreover, the contents of most bioactive ingredients in CHM are low, and some natural products are toxic to humans and animals. Fermentation of CHM could enhance CHM bioactivities and decrease the potential toxicities. The compositions and functions of the microorganisms play essential roles in CHM fermentation, which can affect the fermentation metabolites and pharmaceutical activities of the final fermentation products. During CHM fermentation, probiotics not only increase the contents of bioactive natural products, but also are beneficial for the host gut microbiota and immune system. This review summarizes the advantages of fermentation of CHM using probiotics, fermentation techniques, probiotic strains, and future development for CHM fermentation. Cutting-edge microbiome and synthetic biology tools would harness microbial cell factories to produce large amounts of bioactive natural products derived from CHM with low-cost, which would help speed up modern CHM biomanufacturing.

Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control

Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.

Developments in Fatty Acid-Derived Insect Pheromone Production Using Engineered Yeasts

The use of traditional chemical insecticides for pest control often leads to environmental pollution and a decrease in biodiversity. Recently, insect sex pheromones were applied for sustainable biocontrol of pests in fields, due to their limited adverse impacts on biodiversity and food safety compared to that of other conventional insecticides. However, the structures of insect pheromones are complex, and their chemical synthesis is not commercially feasible. As yeasts have been widely used for fatty acid-derived pheromone production in the past few years, using engineered yeasts may be promising and sustainable for the low-cost production of fatty acid-derived pheromones. The primary fatty acids produced by Saccharomyces cerevisiae and other yeasts are C16 and C18, and it is also possible to rewire/reprogram the metabolic flux for other fatty acids or fatty acid derivatives. This review summarizes the fatty acid biosynthetic pathway in S. cerevisiae and recent progress in yeast engineering in terms of metabolic engineering and synthetic biology strategies to produce insect pheromones. In the future, insect pheromones produced by yeasts might provide an eco-friendly pest control method in agricultural fields.

Genomic Resources to Guide Improvement of the Shea Tree

A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing

The gastrointestinal tract, the largest human microbial reservoir, is highly dynamic. The gut microbes play essential roles in causing colorectal diseases. In the present study, we explored potential keystone taxa during the development of colorectal diseases in central China. Fecal samples of some patients were collected and were allocated to the adenoma (Group A), colorectal cancer (Group C), and hemorrhoid (Group H) groups. The 16S rRNA amplicon and shallow metagenomic sequencing (SMS) strategies were used to recover the gut microbiota. Microbial diversities obtained from 16S rRNA amplicon and SMS data were similar. Group C had the highest diversity, although no significant difference in diversity was observed among the groups. The most dominant phyla in the gut microbiota of patients with colorectal diseases were Bacteroidetes, Firmicutes, and Proteobacteria, accounting for >95% of microbes in the samples. The most abundant genera in the samples were Bacteroides, Prevotella, and Escherichia/Shigella, and further species-level and network analyses identified certain potential keystone taxa in each group. Some of the dominant species, such as Prevotella copri, Bacteroides dorei, and Bacteroides vulgatus, could be responsible for causing colorectal diseases. The SMS data recovered diverse antibiotic resistance genes of tetracycline, macrolide, and beta-lactam, which could be a result of antibiotic overuse. This study explored the gut microbiota of patients with three different types of colorectal diseases, and the microbial diversity results obtained from 16S rRNA amplicon sequencing and SMS data were found to be similar. However, the findings of this study are based on a limited sample size, which warrants further large-scale studies. The recovery of gut microbiota profiles in patients with colorectal diseases could be beneficial for future diagnosis and treatment with modulation of the gut microbiota. Moreover, SMS data can provide accurate species- and gene-level information, and it is economical. It can therefore be widely applied in future clinical metagenomic studies.

Yeast Synthetic Biology for the Production of Lycium barbarum Polysaccharides

The fruit of Lycium barbarum L. (goji berry) is used as traditional Chinese medicine, and has the functions of immune regulation, anti-tumor, neuroprotection, anti-diabetes, and anti-fatigue. One of the main bioactive components is L. barbarum polysaccharide (LBP). Nowadays, LBP is widely used in the health market, and it is extracted from the fruit of L. barbarum. The planting of L. barbarum needs large amounts of fields, and it takes one year to harvest the goji berry. The efficiency of natural LBP production is low, and the LBP quality is not the same at different places. Goji berry-derived LBP cannot satisfy the growing market demands. Engineered Saccharomyces cerevisiae has been used for the biosynthesis of some plant natural products. Recovery of LBP biosynthetic pathway in L. barbarum and expression of them in engineered S. cerevisiae might lead to the yeast LBP production. However, information on LBP biosynthetic pathways and the related key enzymes of L. barbarum is still limited. In this review, we summarized current studies about LBP biosynthetic pathway and proposed the strategies to recover key enzymes for LBP biosynthesis. Moreover, the potential application of synthetic biology strategies to produce LBP using engineered S. cerevisiae was discussed.

Recent Advances on Feasible Strategies for Monoterpenoid Production in Saccharomyces cerevisiae

Terpenoids are a large diverse group of natural products which play important roles in plant metabolic activities. Monoterpenoids are the main components of plant essential oils and the active components of some traditional Chinese medicinal herbs. Some monoterpenoids are widely used in medicine, cosmetics and other industries, and they are mainly obtained by plant biomass extraction methods. These plant extraction methods have some problems, such as low efficiency, unstable quality, and high cost. Moreover, the monoterpenoid production from plant cannot satisfy the growing monoterpenoids demand. The development of metabolic engineering, protein engineering and synthetic biology provides an opportunity to produce large amounts of monoterpenoids eco-friendly using microbial cell factories. This mini-review covers current monoterpenoids production using Saccharomyces cerevisiae. The monoterpenoids biosynthetic pathways, engineering of key monoterpenoids biosynthetic enzymes, and current monoterpenoids production using S. cerevisiae were summarized. In the future, metabolically engineered S. cerevisiae may provide one possible green and sustainable strategy for monoterpenoids supply.

Metabolic Engineering for Glycyrrhetinic Acid Production in Saccharomyces cerevisiae

Glycyrrhetinic acid (GA) is one of the main bioactive components of licorice, and it is widely used in traditional Chinese medicine due to its hepatoprotective, immunomodulatory, anti-inflammatory and anti-viral functions. Currently, GA is mainly extracted from the roots of cultivated licorice. However, licorice only contains low amounts of GA, and the amount of licorice that can be planted is limited. GA supplies are therefore limited and cannot meet the demands of growing markets. GA has a complex chemical structure, and its chemical synthesis is difficult, therefore, new strategies to produce large amounts of GA are needed. The development of metabolic engineering and emerging synthetic biology provide the opportunity to produce GA using microbial cell factories. In this review, current advances in the metabolic engineering of Saccharomyces cerevisiae for GA biosynthesis and various metabolic engineering strategies that can improve GA production are summarized. Furthermore, the advances and challenges of yeast GA production are also discussed. In summary, GA biosynthesis using metabolically engineered S. cerevisiae serves as one possible strategy for sustainable GA supply and reasonable use of traditional Chinese medical plants.

Advances in Metabolic Engineering of Saccharomyces cerevisiae for Cocoa Butter Equivalent Production

Cocoa butter is extracted from cocoa beans, and it is mainly used as the raw material for the production of chocolate and cosmetics. Increased demands and insufficient cocoa plants led to a shortage of cocoa butter supply, and there is therefore much interesting in finding an alternative cocoa butter supply. However, the most valuable component of cocoa butter is rarely available in other vegetable oils. Saccharomyces cerevisiae is an important industrial host for production of chemicals, enzyme and pharmaceuticals. Advances in synthetical biology and metabolic engineering had enabled high-level of triacylglycerols (TAG) production in yeast, which provided possible solutions for cocoa butter equivalents (CBEs) production. Diverse engineering strategies focused on the fatty acid-producing pathway had been applied in S. cerevisiae, and the key enzymes determining the TAG structure were considered as the main engineering targets. Recent development in phytomics and multi-omics technologies provided clues to identify potential targeted enzymes, which are responsible for CBE production. In this review, we have summarized recent progress in identification of the key plant enzymes for CBE production, and discussed recent and future metabolic engineering and synthetic biology strategies for increased CBE production in S. cerevisiae.