Over the past century, Escherichia coli has become one of the best studied organisms on earth. Features such as genetic tractability, favorable growth conditions, well characterized biochemistry and ...physiology, and availability of versatile genetic manipulation tools make E. coli an ideal platform host for development of industrially viable productions. In this review, we discuss the physiological attributes of E. coli that are most relevant for metabolic engineering, as well as emerging techniques that enable efficient phenotype construction. Further, we summarize the large number of native and non-native products that have been synthesized by E. coli, and address some of the future challenges in broadening substrate range and fighting phage infection.
•The well characterized physiology of E. coli allows for rapid strain development.•A plethora of genetic techniques have been developed for genomic edits in E. coli including the λ-Red recombinase system, CRISPR, and MAGE.•A wide variety of chemicals have been produced by E. coli both in the laboratory and for industrial scale production.
Understanding the roles of arbuscular mycorrhizal fungi (AMF) in plant interaction is essential for optimizing plant distribution to restore degraded ecosystems. This study investigated the effects ...of AMF and the presence of legume or grass herbs on phytoremediation with a legume tree, Robinia pseudoacacia, in Pb polluted soil. In monoculture, mycorrhizal dependency of legumes was higher than that of grass, and AMF benefited the plant biomass of legumes but had no effect on grass. Mycorrhizal colonization of plant was enhanced by legume neighbors but inhibited by grass neighbor in co-culture system. N, P, S and Mg concentrations of mycorrhizal legumes were larger than these of non-mycorrhizal legumes. Legume herbs decreased soil pH and thereby increased the Pb concentrations of plants. The neighbor effects of legumes shifted from negative to positive with increasing Pb stress levels, whereas grass provided a negative effect on the growth of legume tree. AMF enhanced the competition but equalized growth of legume-legume under unpolluted and Pb stress conditions, respectively. In conclusion, (1) AMF mediate plant interaction through directly influencing plant biomass, and/or indirectly influencing plant photosynthesis, macronutrient acquisition, (2) legume tree inoculated with AMF and co-planted with legume herbs provides an effective way for Pb phytoremediation.
The discovery and application of genome editing introduced a new era of plant breeding by giving researchers efficient tools for the precise engineering of crop genomes
. Here we demonstrate the ...power of genome editing for engineering broad-spectrum disease resistance in rice (Oryza sativa). We first isolated a lesion mimic mutant (LMM) from a mutagenized rice population. We then demonstrated that a 29-base-pair deletion in a gene we named RESISTANCE TO BLAST1 (RBL1) caused broad-spectrum disease resistance and showed that this mutation caused an approximately 20-fold reduction in yield. RBL1 encodes a cytidine diphosphate diacylglycerol synthase that is required for phospholipid biosynthesis
. Mutation of RBL1 results in reduced levels of phosphatidylinositol and its derivative phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P
). In rice, PtdIns(4,5)P
is enriched in cellular structures that are specifically associated with effector secretion and fungal infection, suggesting that it has a role as a disease-susceptibility factor
. By using targeted genome editing, we obtained an allele of RBL1, named RBL1
, which confers broad-spectrum disease resistance but does not decrease yield in a model rice variety, as assessed in small-scale field trials. Our study has demonstrated the benefits of editing an LMM gene, a strategy relevant to diverse LMM genes and crops.
The aim of this study was to determine whether statin use exerts a protective effect against pancreatic cancer in Type 2 diabetic patients. A retrospective population‐based cohort study was designed ...to analyze the National Health Insurance Research database (NHIRD) from 1997–2010 in Taiwan. A total of 1,140,617 patients with a first‐time diagnosis of Type 2 diabetes were enrolled. The event was defined as newly diagnosed pancreatic cancer. A Cox proportional hazards regression model with time‐dependent covariates was used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) for risk of pancreatic cancer associated with statin use in the diabetic cohort. A total of 2,341 patients with newly diagnosed pancreatic cancer were identified in the diabetic cohort during the follow‐up period of 6,968,217.1 person‐years. In this cohort, 450,282 patients were defined as statin users (statin use ≥28 cumulative defined daily dose cDDD in 1 year) and 0.14% had pancreatic cancer; 690,335 patients were statin nonusers (statin use <28 cDDD in 1 year) and 0.25% had pancreatic cancer. Statin use significantly decreased the risk of pancreatic cancer (adjusted HRs: 0.78 in 28–83 cDDD per year; 0.48 in 84–180 cDDD per year; and 0.33 in >180 cDDD per year) after adjusting for multiple confounders. There was a significant dose‐effect of statin use for the risk of pancreatic cancer (p for trend: <0.001). Statin use may be associated with a reduced risk of pancreatic cancer in Type 2 diabetic patients. More research is needed to clarify this association.
What's new?
Metabolic disturbances are associated with an increased risk of pancreatic cancer, though drugs such as statins, which regulate lipid metabolism, could lower that risk. A unique group in which to investigate potential protective effects are patients with diabetes mellitus, who tend to use statins long‐term or at elevated doses. In this study, statin use was found to significantly reduce the risk of developing pancreatic cancer specifically among patients with chronic type 2 diabetes. The protective effects increased with increasing cumulative daily dose. The ability of statins to reduce pancreatic cancer risk may depend on the presence of diabetes.
.
is a traditional Chinese medicinal plant that is commonly used to treat many ailments. It belongs to the Polygonacae family and grows in northwest and southwest China. At high elevations, the color ...of the plant's young leaves is purple, which gradually changes to green during the growth cycle. Anthraquinone, which is known for various biological activities, is the main bioactive compound in
. Although a significant amount of research has been done on
in the past, the lack of transcriptome data limits our knowledge of the gene regulatory networks involved in pigmentation and in the metabolism of bioactive compounds in
species.
To fill this knowledge gap, we generated high-quality RNA-seq data and performed multi-tissue transcriptomic analyses of
.
We found that three chlorophyll degradation enzymes (
and
) were highly expressed in purple samples, which suggests that the purple pigmentation is mainly due to the effects of chlorophyll degradation. Overall, these data may aid in drafting the transcriptional network in the regulation and biosynthesis of medicinally active compounds in the future.
Siamenoside I is a rare mogroside in Siraitia grosvenorii Swingle and has become one of the target ingredients in natural sweetener production. However, the complex structure of siamenoside I has ...hindered its production in various ways. Here, a yeast cell that produces a specific β-glucosidase for siamenoside I conversion from mogroside V was constructed, and the enzymes were coelectrospun with poly(vinyl alcohol) followed by phenylboronic acid cross-linking to provide potential usage in the batch production process of Siamenoside I. A central composite design (CCD)-response surface methodology (RSM) was used to find the optimum coelectrospinning parameters. The pH stability and sodium dodecyl sulfate tolerance increased for the entrapped enzymes, and positive correlations between the fiber diameter and enzymatic activity were confirmed. The batch process showed an average siamenoside I production rate of 118 ± 0.08 mg L–1 h–1 per gram of fiber. This is the first research article showing specific siamenoside I production on enzyme-loaded electrospun fibers.
BAHD acyltransferases, named after the first four biochemically characterized enzymes of the group, are plant-specific enzymes that catalyze the transfer of coenzyme A-activated donors onto various ...acceptor molecules. They are responsible for the synthesis in plants of a myriad of secondary metabolites, some of which are beneficial for humans either as therapeutics or as specialty chemicals such as flavors and fragrances. The production of pharmaceutical, nutraceutical and commodity chemicals using engineered microbes is an alternative, green route to energy-intensive chemical syntheses that consume petroleum-based precursors. However, identification of appropriate enzymes and validation of their functional expression in heterologous hosts is a prerequisite for the design and implementation of metabolic pathways in microbes for the synthesis of such target chemicals.
For the synthesis of valuable metabolites in the yeast Saccharomyces cerevisiae, we selected BAHD acyltransferases based on their preferred donor and acceptor substrates. In particular, BAHDs that use hydroxycinnamoyl-CoAs and/or benzoyl-CoA as donors were targeted because a large number of molecules beneficial to humans belong to this family of hydroxycinnamate and benzoate conjugates. The selected BAHD coding sequences were synthesized and cloned individually on a vector containing the Arabidopsis gene At4CL5, which encodes a promiscuous 4-coumarate:CoA ligase active on hydroxycinnamates and benzoates. The various S. cerevisiae strains obtained for co-expression of At4CL5 with the different BAHDs effectively produced a wide array of valuable hydroxycinnamate and benzoate conjugates upon addition of adequate combinations of donors and acceptor molecules. In particular, we report here for the first time the production in yeast of rosmarinic acid and its derivatives, quinate hydroxycinnamate esters such as chlorogenic acid, and glycerol hydroxycinnamate esters. Similarly, we achieved for the first time the microbial production of polyamine hydroxycinnamate amides; monolignol, malate and fatty alcohol hydroxycinnamate esters; tropane alkaloids; and benzoate/caffeate alcohol esters. In some instances, the additional expression of Flavobacterium johnsoniae tyrosine ammonia-lyase (FjTAL) allowed the synthesis of p-coumarate conjugates and eliminated the need to supplement the culture media with 4-hydroxycinnamate.
We demonstrate in this study the effectiveness of expressing members of the plant BAHD acyltransferase family in yeast for the synthesis of numerous valuable hydroxycinnamate and benzoate conjugates.
Microbial production of monoterpenoid indole alkaloids (MIAs) provides a sustainable and eco‐friendly means to obtain compounds with high pharmaceutical values. However, efficient biosynthesis of ...MIAs in heterologous microorganisms is hindered due to low supply of key precursors such as geraniol and its derivative 8‐hydroxygeraniol catalyzed by geraniol 8‐hydroxylase (G8H). In this study, we developed a facile evolution platform to screen strains with improved yield of geraniol by using the SCRaMbLE system embedded in the Sc2.0 synthetic yeast and confirmed the causal role of relevant genomic targets. Through genome mining, we identified several G8H enzymes that perform much better than the commonly used CrG8H for 8‐hydroxygeraniol production in vivo. We further showed that the N‐terminus of these G8H enzymes plays an important role in cellular activity by swapping experiments. Finally, the combination of the engineered chassis, optimized biosynthesis pathway, and utilization of G8H led to the final strain with more than 30‐fold improvement in producing 8‐hydroxygeraniol compared with the starting strain. Overall, this study will provide insights into the construction and optimization of yeast cells for efficient biosynthesis of 8‐hydroxygeraniol and its derivatives.
Impact statement
Efficient production of high‐value natural products such as monoterpenoid indole alkaloids in heterologous microorganisms is an important and impactful research field of synthetic biology, which often requires genomic modifications of the chassis and engineering of introduced enzymes. Taking the advantage of the SCRaMbLE system designed in the Sc2.0 synthetic yeast, we developed a facile screening method to identify strain with improved geraniol production after inducible genome rearrangements. We also demonstrated that genome mining of superior enzyme homologs would be an effective and powerful strategy to overcome the rate‐limiting step. These findings expand the current methods to optimize the biosynthesis pathway of 8‐hydroxygeraniol and its derivatives.
The glycosyltransferases (GTs) are an important and functionally diverse family of enzymes involved in glycan and glycoside biosynthesis. Plants have evolved large families of GTs which undertake the ...array of glycosylation reactions that occur during plant development and growth. Based on the Carbohydrate‐Active enZymes (CAZy) database, the genome of the reference plant Arabidopsis thaliana codes for over 450 GTs, while the rice genome (Oryza sativa) contains over 600 members. Collectively, GTs from these reference plants can be classified into over 40 distinct GT families. Although these enzymes are involved in many important plant specific processes such as cell‐wall and secondary metabolite biosynthesis, few have been functionally characterized. We have sought to develop a plant GTs clone resource that will enable functional genomic approaches to be undertaken by the plant research community. In total, 403 (88%) of CAZy defined Arabidopsis GTs have been cloned, while 96 (15%) of the GTs coded by rice have been cloned. The collection resulted in the update of a number of Arabidopsis GT gene models. The clones represent full‐length coding sequences without termination codons and are Gateway® compatible. To demonstrate the utility of this JBEI GT Collection, a set of efficient particle bombardment plasmids (pBullet) was also constructed with markers for the endomembrane. The utility of the pBullet collection was demonstrated by localizing all members of the Arabidopsis GT14 family to the Golgi apparatus or the endoplasmic reticulum (ER). Updates to these resources are available at the JBEI GT Collection website http://www.addgene.org/.
In nature, metabolic pathways are often organized into complex structures such as multienzyme complexes, enzyme molecular scaffolds, or reaction microcompartments. These structures help facilitate ...multi-step metabolic reactions. However, engineered metabolic pathways in microbial cell factories do not possess inherent metabolic regulatory mechanisms, which can result in metabolic imbalance. Taking inspiration from nature, scientists have successfully developed synthetic scaffolds to enhance the performance of engineered metabolic pathways in microbial cell factories. By recruiting enzymes, synthetic scaffolds facilitate the formation of multi-enzyme complexes, leading to the modulation of enzyme spatial distribution, increased enzyme activity, and a reduction in the loss of intermediate products and the toxicity associated with harmful intermediates within cells. In recent years, scaffolds based on proteins, nucleic acids, and various organelles have been developed and employed to facilitate multiple metabolic pathways. Despite varying degrees of success, synthetic scaffolds still encounter numerous challenges. The objective of this review is to provide a comprehensive introduction to these synthetic scaffolds and discuss their latest research advancements and challenges.
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