Avermectin B1a production in Streptomyces avermitilis is enhanced by engineering aveC and precursor supply genes

Avermectins and Their Derivatives: Recent Advances in Biosynthesis and Application

Avermectins (AVMs) and their derivatives are the most effective and widely used nematicides, insecticides, and acaricides against endo- and ectoparasites of plants, animals, and humans. Demand for avermectins and their highly effective derivatives has increased due to their high cost-effectiveness and wide range of applications as medicines and crop protection products. Due to the unique structures of these compounds and for industrial production purposes, numerous efforts and strategies have been dedicated to enhancing the production of avermectins and creating new analogues in recent years. Here, we have systemically reviewed the recent studies on the biosynthesis and application of avermectins and their derivatives, including avermectin metabolism and its related bioregulation in Streptomyces avermitilis, approaches for enhancing the bioproduction of avermectins, the structure and toxicology of avermectin derivatives, and future prospects, with a focus on the recent advances in biosynthesis and significance of the superior avermectin derivatives.

Genome Combination Improvement Strategy Promotes Efficient Spinosyn Biosynthesis in Saccharopolyspora spinosa

Spinosyns are secondary metabolites produced by Saccharopolyspora spinosa known for their potent insecticidal properties and broad pesticidal spectrum. We report significant advancements in spinosyn biosynthesis achieved through a genome combination improvement strategy in S. spinosa. By integrating modified genome shuffling with ultraviolet mutation and multiomics analysis, we developed a high-yield spinosyn strain designated as YX2. The levels of most proteins and metabolites linked to primary metabolism and spinosyn biosynthesis were greater in this strain than those in S. spinosa. Based on these insights, we overexpressed 15 relevant functional genes to enhance the conversion of fatty acids into acetyl-coenzyme A. Notably, the overexpression of acd (YX2_3432) significantly increased the spinosyn yield, reaching 1120 ± 108 mg/L, which is about 12 times higher than that produced by S. spinosa. This study presents a valuable and straightforward strategy that can be broadly applied to enhance the production of secondary metabolites in actinomycetes.

Combinatorial metabolic engineering strategy of precursor pools for the yield improvement of spinosad in Saccharopolyspora spinosa

Spinosad is an insecticide produced by Saccharopolyspora spinosa, and its larvicidal activity is considered a promising approach to combat crop pests. The aim of this study was to enhance the synthesis of spinosad through increasing the supply of acyl-CoAs precursor by the following steps. (i) Engineering the β-oxidation pathway by overexpressing key genes within the pathway to promote the synthesis of spinosad. The results showed that the overexpression of fadD, fadE, and fadA1 genes, as well as the co-expression of fadA1 and fadE genes, increased the yield of spinosad by 0.36-fold, 0.89-fold, 0.75-fold and 1.25-fold respectively. (ii) Employing combinatorial engineering of the β-oxidation pathway and ACC/PCC pathway to promote the synthesis of spinosad. The results showed that the co-expression of fadE and pccA, as well as accC and fadE, resulted in a 1.77-fold and 1.43-fold increase in spinosad production respectively. (iii) When exogenous triacylglycerol was added to the fermentation medium, the solely engineering of the β-oxidation pathway increased the yield of spinosad by 7.13-fold, reaching 427.23 mg/L. While the combinatorial engineering of both the β-oxidation pathway and ACC/PCC pathway increased the yield of spinosad by 9.61-fold, reaching 625.17 mg/L, and further optimization of the culture medium resulted in an even higher yield of spinosad, reaching 1293.43 mg/L. The results of this study indicate that the above combination strategy can promote the efficient biosynthesis of spinosad.

Enhanced triacylglycerol metabolism contributes to the efficient biosynthesis of spinosad in Saccharopolyspora spinosa

Triacylglycerol (TAG) is crucial for antibiotic biosynthesis derived from Streptomyces, as it serves as an important carbon source. In this study, the supplementation of exogenous TAG led to a 3.92-fold augmentation in spinosad production. The impact of exogenous TAG on the metabolic network of Saccharopolyspora spinosa were deeply analyzed through comparative proteomics. To optimize TAG metabolism and enhance spinosad biosynthesis, the lipase-encoding genes lip886 and lip385 were overexpressed or co-expressed. The results shown that the yield of spinosad was increased by 0.8-fold and 0.4-fold when lip886 and lip385 genes were overexpressed, respectively. Synergistic co-expression of these genes resulted in a 2.29-fold increase in the yield of spinosad. Remarkably, the combined overexpression of lip886 and lip385 in the presence of exogenous TAG elevated spinosad yields by 5.5-fold, led to a drastic increase in spinosad production from 0.036 g/L to 0.234 g/L. This study underscores the modification of intracellular concentrations of free fatty acids (FFAs), short-chain acyl-CoAs, ATP, and NADPH as mechanisms by which exogenous TAG modulates spinosad biosynthesis. Overall, the findings validate the enhancement of TAG catabolism as a beneficial strategy for optimizing spinosad production and provide foundational insights for engineering secondary metabolite biosynthesis pathways in another Streptomyces.

Metabolic engineering of Streptomyces roseosporus for increased production of clinically important antibiotic daptomycin

Daptomycin (DAP), a novel cyclic lipopeptide antibiotic produced by Streptomyces roseosporus, is clinically important for treatment of infections caused by multidrug-resistant Gram-positive pathogens, but the low yield hampers its large-scale industrial production. Here, we describe a combination metabolic engineering strategy for constructing a DAP high-yielding strain. Initially, we enhanced aspartate (Asp) precursor supply in S. roseosporus wild-type (WT) strain by separately inhibiting Asp degradation and competitive pathway genes using CRISPRi and overexpressing Asp synthetic pathway genes using strong promoter kasOp*. The resulting strains all showed increased DAP titre. Combined inhibition of acsA4, pta, pyrB, and pyrC increased DAP titre to 167.4 μg/mL (73.5% higher than WT value). Co-overexpression of aspC, gdhA, ppc, and ecaA led to DAP titre 168 μg/mL (75.7% higher than WT value). Concurrently, we constructed a chassis strain favourable for DAP production by abolishing by-product production (i.e., deleting a 21.1 kb region of the red pigment biosynthetic gene cluster (BGC)) and engineering the DAP BGC (i.e., replacing its native dptEp with kasOp*). Titre for the resulting chassis strain reached 185.8 μg/mL. Application of our Asp precursor supply strategies to the chassis strain further increased DAP titre to 302 μg/mL (2.1-fold higher than WT value). Subsequently, we cloned the engineered DAP BGC and duplicated it in the chassis strain, leading to DAP titre 274.6 μg/mL. The above strategies, in combination, resulted in maximal DAP titre 350.7 μg/mL (2.6-fold higher than WT value), representing the highest reported DAP titre in shake-flask fermentation. These findings provide an efficient combination strategy for increasing DAP production and can also be readily applied in the overproduction of other Asp-related antibiotics.

Potential of Streptomyces avermitilis: A Review on Avermectin Production and Its Biocidal Effect

Secondary metabolites produced by the fermentation of Streptomyces avermitilis bacterium are powerful antiparasitic agents used in animal health, agriculture and human infection treatments. Avermectin is a macrocyclic lactone with four structural components (A1, A2, B1, B2), each of them containing a major and a minor subcomponent, out of which avermectin B1a is the most effective parasitic control compound. Avermectin B1a produces two homologue avermectins (B1 and B2) that have been used in agriculture as pesticides and antiparasitic agents, since 1985. It has a great affinity with the Cl-channels of the glutamate receptor, allowing the constant flow of Cl- ions into the nerve cells, causing a phenomenon of hyperpolarization causing death by flaccid paralysis. The purpose of this work was to gather information on the production of avermectins and their biocidal effects, with special emphasis on their role in the control of pests and phytopathogenic diseases. The literature showed that S. avermitilis is an important producer of macrocyclic lactones with biocidal properties. In addition, avermectin contributes to the control of ectoparasites and endoparasites in human health care, veterinary medicine and agriculture. Importantly, avermectin is a compound that is harmless to the host (no side effects), non-target organisms and the environment.

Influence of Cluster-Situated Regulator PteF in Filipin Biosynthetic Cluster on Avermectin Biosynthesis in Streptomyces avermitilis

Crosstalk regulation is widespread in Streptomyces species. Elucidating the influence of a specific regulator on target biosynthetic gene clusters (BGCs) and cell metabolism is crucial for strain improvement through regulatory protein engineering. PteF and PteR are two regulators that control the biosynthesis of filipin, which competes for building blocks with avermectins in Streptomyces avermitilis. However, little is known about the effects of PteF and PteR on avermectin biosynthesis. In this study, we investigated their impact on avermectin biosynthesis and global cell metabolism. The deletion of pteF resulted in a 55.49% avermectin titer improvement, which was 23.08% higher than that observed from pteR deletion, suggesting that PteF plays a more significant role in regulating avermectin biosynthesis, while PteF hardly influences the transcription level of genes in avermectin and other polyketide BGCs. Transcriptome data revealed that PteF exhibited a global regulatory effect. Avermectin production enhancement could be attributed to the repression of the tricarboxylic acid cycle and fatty acid biosynthetic pathway, as well as the enhancement of pathways supplying acyl-CoA precursors. These findings provide new insights into the role of PteF on avermectin biosynthesis and cell metabolism, offering important clues for designing and building efficient metabolic pathways to develop high-yield avermectin-producing strains.

Enhancement of acyl-CoA precursor supply for increased avermectin B1a production by engineering meilingmycin polyketide synthase and key primary metabolic pathway genes

Avermectins (AVEs), a family of macrocyclic polyketides produced by Streptomyces avermitilis, have eight components, among which B1a is noted for its strong insecticidal activity. Biosynthesis of AVE "a" components requires 2-methylbutyryl-CoA (MBCoA) as starter unit, and malonyl-CoA (MalCoA) and methylmalonyl-CoA (MMCoA) as extender units. We describe here a novel strategy for increasing B1a production by enhancing acyl-CoA precursor supply. First, we engineered meilingmycin (MEI) polyketide synthase (PKS) for increasing MBCoA precursor supply. The loading module (using acetyl-CoA as substrate), extension module 7 (using MMCoA as substrate) and TE domain of MEI PKS were assembled to produce 2-methylbutyrate, providing the starter unit for B1a production. Heterologous expression of the newly designed PKS (termed Mei-PKS) in S. avermitilis wild-type (WT) strain increased MBCoA level, leading to B1a titer 262.2 μg/mL - 4.36-fold higher than WT value (48.9 μg/mL). Next, we separately inhibited three key nodes in essential pathways using CRISPRi to increase MalCoA and MMCoA levels in WT. The resulting strains all showed increased B1a titer. Combined inhibition of these key nodes in Mei-PKS expression strain increased B1a titer to 341.9 μg/mL. Overexpression of fatty acid β-oxidation pathway genes in the strain further increased B1a titer to 452.8 μg/mL - 8.25-fold higher than WT value. Finally, we applied our precursor supply strategies to high-yield industrial strain A229. The strategies, in combination, led to B1a titer 8836.4 μg/mL - 37.8% higher than parental A229 value. These findings provide an effective combination strategy for increasing AVE B1a production in WT and industrial S. avermitilis strains, and our precursor supply strategies can be readily adapted for overproduction of other polyketides.

Novel strategy for depolymerization of avermectin fermentation residue to value-added amino acid product

Avermectin fermentation residue (AFR) is rich in proteins, which can be depolymerized to value-added amino acids for in-plant reuse. The hydrochloric acid (HCl) hydrolysis is performed and investigated under different conditions, including HCl concentration, solid-liquid ratio, temperature, and time. The hydrolysis degree (HD) of 67.7% can be achieved. The empirical correlation of HD is established with a good practicability to control the HD and predict the experimental conditions. Solid-liquid reaction is confirmed to be dominant during the hydrolysis process. There are 17 kinds of amino acids in the hydrolysate, benefiting the reuse. Avermectin is not detected in the hydrolysate and AFR, and the mass of AFR is reduced by 53.8 wt%. This work provides a novel strategy for the environmentally friendly treatment and meanwhile the resource recovery of AFR.

Enhancing tylosin production by combinatorial overexpression of efflux, SAM biosynthesis, and regulatory genes in hyperproducing Streptomyces xinghaiensis strain

Tylosin is a 16-membered macrolide antibiotic widely used in veterinary medicine to control infections caused by Gram-positive pathogens and mycoplasmas. To improve the fermentation titer of tylosin in the hyperproducing Streptomyces xinghaiensis strain TL01, we sequenced its whole genome and identified the biosynthetic gene cluster therein. Overexpression of the tylosin efflux gene tlrC, the cluster-situated S-adenosyl methionine (SAM) synthetase gene metK_cs, the SAM biosynthetic genes adoK_cs-metF_cs, or the pathway-specific activator gene tylR enhanced tylosin production by 18%, 12%, 11%, and 11% in the respective engineered strains TLPH08-2, TLPH09, TLPH10, and TLPH12. Co-overexpression of metK_cs and adoK_cs-metF_cs as two transcripts increased tylosin production by 22% in the resultant strain TLPH11 compared to that in TL01. Furthermore, combinational overexpression of tlrC, metK_cs, adoK_cs-metF_cs, and tylR as four transcripts increased tylosin production by 23% (10.93g/L) in the resultant strain TLPH17 compared to that in TL01. However, a negligible additive effect was displayed upon combinational overexpression in TLPH17 as suggested by the limited increment of fermentation titer compared to that in TLPH08-2. Transcription analyses indicated that the expression of tlrC and three SAM biosynthetic genes in TLPH17 was considerably lower than that of TLPH08-2 and TLPH11. Based on this observation, the five genes were rearranged into one or two operons to coordinate their overexpression, yielding two engineered strains TLPH23 and TLPH24, and leading to further enhancement of tylosin production over TLPH17. In particular, the production of TLPH23 reached 11.35 g/L. These findings indicated that the combinatorial strategy is a promising approach for enhancing tylosin production in high-yielding industrial strains.

Avermectin B1a Shows Potential Anti-Proliferative and Anticancer Effects in HCT-116 Cells via Enhancing the Stability of Microtubules

Avermectins are a group of macrocyclic lactones that are commonly used as pesticides to treat pests and parasitic worms. Some members of the avermectin family, such as ivermectin, have been found to exhibit anti-proliferative activity toward cancer cells. This study aimed to investigate the potential anti-cancer activities of avermectin B1a using the HCT-116 colon cancer cell line. The MTT assay was used to calculate the IC50 by incubating cells with increasing doses of avermectin B1a for 24, 48, and 72 h. Flow cytometry was used to evaluate apoptosis following the 24 h incubation of cells. The migration capacity of the HCT-116 cells in the absence or presence of avermectin B1a was also investigated. Finally, tubulin polymerization in the presence of avermectin B1a was evaluated. Avermectin B1a presented anti-proliferative activity with an IC50 value of 30 μM. Avermectin B1a was found to promote tubulin polymerization at 30 μM. In addition, avermectin B1a induced apoptosis in HCT-116 cells and substantially diminished their ability to migrate. Avermectin B1a exhibits significant anti-cancer activity and enhances tubulin polymerization, suggesting that it can be used as a promising microtubule-targeting agent for the development of future anticancer drugs.

Natural nematicidal metabolites and advances in their biocontrol capacity on plant parasitic nematodes

Covering: 2010 to 2021Natural nematicidal metabolites are important sources of nematode control. This review covers the isolation and structural determination of nematicidal metabolites from 2010 to 2021. We summarise chemical structures, bioactivity, metabolic regulation and biosynthesis of potential nematocides, and structure-activity relationship and application potentiality of natural metabolites in plant parasitic nematodes' biocontrol. In doing so, we aim to provide a comprehensive overview of the potential roles that natural metabolites can play in anti-nematode strategies.

Modular polyketide synthase-derived insecticidal agents: from biosynthesis and metabolic engineering to combinatorial biosynthesis for their production

Covering: up to 2022Polyketides derived from actinomycetes are a valuable source of eco-friendly biochemical insecticides. The development of new insecticides is urgently required, as the number of insects resistant to more than one drug is rapidly increasing. Moreover, significant enhancement of the production of such biochemical insecticides is required for economical production. There has been considerable improvement in polyketide insecticidal agent production and development of new insecticides. However, most commercially important biochemical insecticides are synthesized by modular type I polyketide synthases (PKSs), and their structural complexities make chemical modification challenging. A detailed understanding of the biosynthetic mechanisms of potent polyketide insecticides and the structure-activity relationships of their analogs will provide insight into the comprehensive design of new insecticides with improved efficacies. Further metabolic engineering and combinatorial biosynthesis efforts, reinvigorated by synthetic biology, can eventually produce designed analogs in large quantities. This highlight reviews the biosynthesis of representative insecticides produced by modular type I PKSs, such as avermectin, spinosyn, and spectinabilin, and their insecticidal properties. Metabolic engineering and combinatorial biosynthetic strategies for the development of high-yield strains and analogs with insecticidal activities are emphasized, proposing a way to develop a next-generation insecticide.

Acyltransferase Domain Swapping for the Production of Tenvermectin B Metabolites in Genetically Engineered Strain Streptomyces avermitilis HU02

Tenvermectins A and B (TVMs A and B) are hybrid natural compounds of avermectins and milbemycins with enhanced insecticidal activity. Aiming at obtaining a strain for the production of the higher activity metabolite-TVM-B as a major constituent, a recombinant strain Streptomyces avermitilis HU02 was constructed by a domain swapping strategy in which milA1-AT0 gene in S. avermitilis MHJ1011 was replaced by eryA1-AT0 gene from Saccharopolyspora erythraea ATCC 40137. Chemical investigation on the culture of S. avermitilis HU02 led to the isolation of a large amount of TVM-B and trace amounts of five new TVM-B analogues. The structures of new metabolites were elucidated by extensive spectroscopic analysis including 1D and 2D nuclear magnetic resonance and high-resolution electrospray ionization mass spectrometry data. The bioassay test indicated that five new TVM-B analogues exhibited potent insecticidal activity against Tetranychus cinnabarinus and Bursaphelenchus xylophilus. This study provided a feasible route to the low-cost production of TVM-B and enriched the structural diversity of TVM-B metabolites.