Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens.

BACKGROUND: Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area. RESULTS: Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation. CONCLUSIONS: Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.

Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals.

BACKGROUND: In our previous study, Citrobacter sp. XT1-2-2 was isolated from high cadmium-contaminated soils, and demonstrated an excellent ability to decrease the bioavailability of cadmium in the soil and inhibit cadmium uptake in rice. In addition, the strain XT1-2-2 could significantly promote rice growth and increase rice biomass. Therefore, the strain XT1-2-2 shows great potential for remediation of cadmium -contaminated soils. However, the genome sequence of this organism has not been reported so far.  RESULTS: Here the basic characteristics and genetic diversity of the strain XT1-2-2 were described, together with the draft genome and comparative genomic results. The strain XT1-2-2 is 5040459 bp long with an average G + C content of 52.09%, and contains a total of 4801 genes. Putative genomic islands were predicted in the genome of Citrobacter sp. XT1-2-2. All genes of a complete set of sulfate reduction pathway and various putative heavy metal resistance genes in the genome were identified and analyzed. CONCLUSIONS: These analytical results provide insights into the genomic basis of microbial immobilization of heavy metals.

Effects of acuC on the growth development and spinosad biosynthesis of Saccharopolyspora spinosa.

BACKGROUND: Acetoin utilization protein (acuC) is a type I histone deacetylase which is highly conserved in bacteria. The acuC gene is related to the acetylation/deacetylation posttranslational modification (PTM) system in S. spinosa. Spinosyns, the secondary metabolites produced by Saccharopolyspora spinosa, are the active ingredients in a family of insect control agents. However, the specific functions and influences of acuC protein in S. spinosa are yet to be characterized. RESULTS: The knockout strain and overexpression strain were constructed separately with the shuttle vector pOJ260. The production of spinosyns A and D from S. spinosa-acuC were 105.02 mg/L and 20.63 mg/L, which were 1.82-fold and 1.63-fold higher than those of the wild-type strain (57.76 mg/L and 12.64 mg/L), respectively. The production of spinosyns A and D from S. spinosa-ΔacuC were 32.78 mg/L and 10.89 mg/L, respectively. The qRT-PCR results of three selected genes (bldD, ssgA and whiA) confirmed that the overexpression of acuC affected the capacities of mycelial differentiation and sporulation. Comparative proteomics analysis was performed on these strains to investigate the underlying mechanism leading to the enhancement of spinosad yield. CONCLUSIONS: This study first systematically analysed the effects of overexpression acuC on the growth of S. spinosa and the production of spinosad. The results identify the differentially expressed proteins and provide evidences to understand the acetylation metabolic mechanisms which can lead to the increase of secondary metabolites.

Bacterioferritin: a key iron storage modulator that affects strain growth and butenyl-spinosyn biosynthesis in Saccharopolyspora pogona.

BACKGROUND: Butenyl-spinosyn, produced by Saccharopolyspora pogona, is a promising biopesticide due to excellent insecticidal activity and broad pesticidal spectrum. Bacterioferritin (Bfr, encoded by bfr) regulates the storage and utilization of iron, which is essential for the growth and metabolism of microorganisms. However, the effect of Bfr on the growth and butenyl-spinosyn biosynthesis in S. pogona has not been explored. RESULTS: Here, we found that the storage of intracellular iron influenced butenyl-spinosyn biosynthesis and the stress resistance of S. pogona, which was regulated by Bfr. The overexpression of bfr increased the production of butenyl-spinosyn by 3.14-fold and enhanced the tolerance of S. pogona to iron toxicity and oxidative damage, while the knockout of bfr had the opposite effects. Based on the quantitative proteomics analysis and experimental verification, the inner mechanism of these phenomena was explored. Overexpression of bfr enhanced the iron storage capacity of the strain, which activated polyketide synthase genes and enhanced the supply of acyl-CoA precursors to improve butenyl-spinosyn biosynthesis. In addition, it induced the oxidative stress response to improve the stress resistance of S. pogona. CONCLUSION: Our work reveals the role of Bfr in increasing the yield of butenyl-spinosyn and enhancing the stress resistance of S. pogona, and provides insights into its enhancement on secondary metabolism, which provides a reference for optimizing the production of secondary metabolites in actinomycetes.

Effect of the TetR family transcriptional regulator Sp1418 on the global metabolic network of Saccharopolyspora pogona.

BACKGROUND: Saccharopolyspora pogona is a prominent industrial strain due to its production of butenyl-spinosyn, a high-quality insecticide against a broad spectrum of insect pests. TetR family proteins are diverse in a tremendous number of microorganisms and some are been researched to have a key role in metabolic regulation. However, specific functions of TetR family proteins in S. pogona are yet to characterize. RESULTS: In the present study, the overexpression of the tetR-like gene sp1418 in S. pogona resulted in marked effects on vegetative growth, sporulation, butenyl-spinosyn biosynthesis, and oxidative stress. By using qRT-PCR analysis, mass spectrometry, enzyme activity detection, and sp1418 knockout verification, we showed that most of these effects could be attributed to the overexpression of Sp1418, which modulated enzymes related to the primary metabolism, oxidative stress and secondary metabolism, and thereby resulted in distinct growth characteristics and an unbalanced supply of precursor monomers for butenyl-spinosyn biosynthesis. CONCLUSION: This study revealed the function of Sp1418 and enhanced the understanding of the metabolic network in S. pogona, and provided insights into the improvement of secondary metabolite production.

Impact on strain growth and butenyl-spinosyn biosynthesis by overexpression of polynucleotide phosphorylase gene in Saccharopolyspora pogona.

Polynucleotide phosphorylase is a highly conserved protein found in bacteria and fungi that can regulate the transcription of related enzymes involved in amino acid metabolism, organic acid metabolism, and cell biosynthesis. We studied the effect of polynucleotide phosphorylase on Saccharopolyspora pogona (S. pogona) growth and the synthesis of secondary metabolites. First, we generated the overexpression vector pOJ260-PermE-pnp via overlap extension PCR. The vector pOJ260-PermE-pnp was then introduced into S. pogona by conjugal transfer, thereby generating the recombination strain S. pogona-Pnp. Results showed that engineering strains possessed higher biomass than those of the wild-type strains. Moreover, the ability of these strains to produce spores on solid medium was stronger than that of the wild-type strains. HPLC results revealed that the butenyl-spinosyn yield in S. pogona-Pnp increased by 1.92-fold compared with that of S. pogona alone. These findings revealed that overexpression of polynucleotide phosphorylase effectively promoted butenyl-spinosyn biosynthesis in S. pogona. This result may be extended to other Streptomyces for strain improvement.

Sound-Triggered Production of Antiaggregation Pheromone Limits Overcrowding of Dendroctonus valens Attacking Pine Trees.

For insects that aggregate on host plants, both attraction and antiaggregation among conspecifics can be important mechanisms for overcoming host resistance and avoiding overcrowding, respectively. These mechanisms can involve multiple sensory modalities, such as sound and pheromones. We explored how acoustic and chemical signals are integrated by the bark beetle Dendroctonus valens to limit aggregation in China. In its native North American range, this insect conducts nonlethal attacks on weakened trees at very low densities, but in its introduced zone in China, it uses mixtures of host tree compounds and the pheromone component frontalin to mass attack healthy trees. We found that exo-brevicomin was produced by both female and male D. valens, and that this pheromone functioned as an antiaggregating signal. Moreover, beetles feeding in pairs or in masses were more likely than were beetles feeding alone to produce exo-brevicomin, suggesting a potential role of sound by neighboring beetles in stimulating exo-brevicomin production. Sound playback showed that an agreement sound was produced by both sexes when exposed to the aggregation pheromone frontalin and attracts males, and an aggressive sound was produced only by males behaving territorially. These signals triggered the release of exo-brevicomin by both females and males, indicating an interplay of chemical and sonic communication. This study demonstrates that the bark beetle D. valens uses sounds to regulate the production of an antiaggregation pheromone, which may provide new approaches to pest management of this invasive species.

Oral secretions from Mythimna separata insects specifically induce defence responses in maize as revealed by high-dimensional biological data.

Attack from insect herbivores poses a major threat to plant survival, and accordingly, plants have evolved sophisticated defence systems. Maize is cultivated as a staple crop worldwide, and insect feeding causes large production losses. Despite its importance in agriculture, little is known about how maize reacts to insect herbivory. Taking advantage of advances in sequencing and mass spectrometry technology, we studied the response of maize to mechanical wounding and simulated Mythimna separata (a specialist insect) herbivory by applying its oral secretions (OS) to wounds. In comparison to the responses induced by mechanical wounding, OS elicited larger and longer-lasting changes in the maize transcriptome, proteome, metabolome and phytohormones. Specifically, many genes, proteins and metabolites were uniquely induced or repressed by OS. Nearly 290 transcription factor genes from 39 families were involved in OS-induced responses, and among these, more transcription factor genes were specifically regulated by OS than by wounding. This study provides a large-scale omics dataset for understanding maize response to chewing insects and highlights the essential role of OS in plant-insect interactions.

The pheromone frontalin and its dual function in the invasive bark beetle Dendroctonus valens.

The red turpentine beetle, Dendroctonus valens LeConte, is one of the most destructive invasive forest pests in China, having killed more than 6 million pines since its first outbreak in 1999. Little is known about D. valens pheromone biology and no aggregation pheromone has yet been identified. Analysis by gas chromatograph/mass spectrometer of volatiles collected from live beetles in China showed that female beetles produce frontalin and males do not. Olfactory assays in the laboratory showed that males were attracted to frontalin at a wide range of concentrations, whereas females were attracted to it at a narrow range of concentrations. In field trials, 3-carene, a monoterpene kairomone from a pine tree selected to host the beetles attracted both sexes, and when frontalin was added, the total number of beetles captured increased by almost 200%. However, increasing concentrations of frontalin significantly decreased the percentage of female beetles trapped. These results suggest a new role of frontalin as an aggregation pheromone in addition to a female-produced sex pheromone, which was previously shown in a North American population. The dual functions of the pheromone frontalin produced by D. valens females, as well as its ecological significance for overcoming host resistance, are discussed.

Corn defense responses to nitrogen availability and subsequent performance and feeding preferences of beet armyworm (Lepidoptera: Noctuidae).

Many studies have reported the effect of nitrogen (N) fertilization on plant constitutive defense responses; however, little is known about their effects on plant induced defense patterns and its consequence for insect herbivores. In our experiments, the effects of N availability on growth, nutritional quality (N content, protein/carbohydrate [P:C] ratio, modified gross energy [MGE]), and constitutive phenolics of corn, Zea mays L. were quantified. Moreover, the indirect effects of N fertilization on the beet armyworm, Spodoptera exigua Hübner through larval performance and feeding preference were examined. N fertilization increased plant growth, and depressed defense traits by increasing N content and the P:C ratio, as well as decreasing the constitutive concentration of phenolics. Subsequently, beet armyworm showed higher performance and preferentially fed on high-N corn because of its low defense traits. After beet armyworm feeding, high-N corn significantly deterred larval feeding, and had negative effects on the performance of beet armyworm through decreasing P:C ratio and increasing induced phenolics. On the contrary, there were no significant changes in P:C ratio and phenolics in low-N corn after feeding damage. Larval performance and preference were also not affected by induced compounds in low-N corn, which suggested that the expression of induced defense was dependent on N availability. The result indicates that N availability can exert a variety of bottom-up effect on plant defense patterns to influence insect population dynamics, and thereby may represent a source of variation in plant-insect interactions.

Identification and functional analysis of odorant-binding proteins of the parasitoid wasp Scleroderma guani reveal a chemosensory synergistic evolution with the host Monochamus alternatus.

Scleroderma guani is a generalist ectoparasitoid of wood-boring insects. The chemosensory genes expressed in its antennae play crucial roles in host-seeking. In the present study, we identified 14 OBP genes for the first time from the antennae transcriptomes and genomic data of S. guani. The expression profiles of 14 OBPs were tested by RT-qPCR, and the RT-qPCR results showed that SguaOBP2/5/6/11/12/13 were specifically highly expressed in the female antennae. Then we performed ligand binding assays to test the interactions between six selected SguaOBPs with host specific chemical compounds from M. alternatus and pines. The binding results indicated that SguaOBP12 had a higher binding affinity with longifolene, ß-caryophyllene, α-pinene, ß-pinene, myrcene, butylated hydroxytoluene, and 3-carene. SguaOBP11 had a high or medium binding affinity with them. Furthermore, both SguaOBP11 and SguaOBP12 had a medium binding affinity with the aggregation pheromone of Monochamus species, 2-undecyloxy-1-ethanol. Finally, by using molecular docking and RNAi, we further explored the molecular interactions and behavioral functions of SguaOBP11 and SguaOBP12 with these vital odor molecules. Our study contributes to the further understanding of chemical communications between S. guani and its host, and further exploration for its role as a more effective biological control agent.

Adaptive Reproductive Strategies of an Ectoparasitoid Sclerodermus guani under the Stress of Its Entomopathogenic Fungus Beauveria bassiana.

Complex interspecific relationships between parasites and their insect hosts involve multiple factors and are affected by their ecological and evolutionary context. A parasitoid Sclerodermus guani (Hymenoptera: Bethylidae) and an entomopathogenic fungus Beauveria bassiana (Hypocreales: Cordycipitaceae) shared the same host in nature, Monochamus alternatus (Coleoptera: Cerambycidae). They often encountered the semi-enclosed microhabitat of the host larvae or pupae. We tested the survival and reproduction of the parasitoid's parent and its offspring fitness under different concentrations of B. bassiana suspension. The results show that S. guani parent females carrying higher concentrations of the pathogen shorten the pre-reproductive time and regulate their own fertility and their offspring's survival and development. This minimal model of the interspecific interactions contains three dimensionless parameters, vulnerability (θ), dilution ratio (δ), and PR, which were used to evaluate the mortality effect of the parasitoid S. guani on its host M. alternatus under the stress of the entomopathogenic fungus B. bassiana. We compared the infection and lethal effect of the fungus B. bassiana with different concentrations to the parasitoid S. guani and the host larvae M. alternatus. At higher concentrations of the pathogen, the parasitoid parent females shorten the pre-reproductive time and regulate their own fertility and their offspring's survival and development. At moderate concentrations of the pathogen, however, the ability of the parasitoid to exploit the host is more flexible and efficient, possibly reflecting the potential interspecific interactions between the two parasites which were able to coexist and communicate with their hosts in ecological contexts (with a high overlap in time and space) and cause interspecific competition and intraguild predation.

Trade-offs of host use between generalist and specialist Helicoverpa sibling species: adult oviposition and larval performance.

Much attention has been paid to the question of the relative importance of female behaviour versus larval feeding capacities in determining the host range of herbivorous insects. Host-use trade-offs displayed by generalist and specialist sister species of the genus Helicoverpa were evaluated to examine the relationship between maternal choice and offspring performance. The prediction of optimal oviposition theory, that females will choose to lay eggs on plants on which their offspring perform best as larvae, was tested by measuring oviposition preference and larval performance of Helicoverpa armigera and H. assulta on tobacco, sunflower, and hot pepper. These two measures were more highly correlated in the specialist H. assulta. Both species exhibited the same oviposition preference ranking: tobacco > sunflower > hot pepper. H. armigera larvae preferred sunflower, followed by tobacco and hot pepper; while H. assulta larvae preferred tobacco to sunflower and hot pepper, consistent with their mothers' oviposition preference. Duration of the total period from egg to adult emergence for each species was significantly shorter on the host plant preferred by the larvae. H. assulta had shorter larval duration and higher relative growth rate than H. armigera on tobacco and hot pepper, and vice versa for sunflower, indicating species differences in host utilization. Thus, while only the specialist H. assulta displayed the predicted optimal oviposition pattern, females of both species show the least preference for the plant on which their offspring perform worst. Selection for optimal oviposition may be stronger on the specialist, which has fewer choices and lower lifetime fecundity than the generalist.

Fighting and aggressive sound determines larger male to win male-male competition in a bark beetle.

Intrasexual selection occurs in male-male competition over access to females and usually results in the larger male winning. While much research has documented that size matters, little is known about how the larger male wins. Dendroctonus valens is an aggregating monogamous bark beetle in which males have large variation in body size and display intense competition over females. Behavioral observation showed two males fight each other within the gallery by pushing/shoving and stridulated more when two males encountered each other. Experiments using two different-sized males synchronously competing showed that larger males won 95% of contests. Reciprocal displacement experiments using muted and intact males of different or equal size were used to simulate male-male competition. Larger males displaced the smaller resident male in 90% of contests, while smaller males prevailed over larger residents in 6.7% of contests. With both males silenced, larger males displaced smaller males in 80% of contests, while smaller males prevailed in 8% of contests. Further experiments using equal-sized males showed aggressive sound-emitting males displaced muted males in 67% of contests, yet intact males displaced other intact males in only 37.5% of contests. Sound analysis showed sound pressure level is an honest signal of body size and males chose soft sounds over loud aggressive sounds in assays. Therefore, D. valens males have evolved dual behaviors, fighting and aggressive sounds associated with body size, to assess rivals to compete for a partner, gaining insights in male-male competition for this species and for other animals.

Flaviolin-Like Gene Cluster Deletion Optimized the Butenyl-Spinosyn Biosynthesis Route in Saccharopolyspora pogona.

Reduction and optimization of the microbial genome is an important strategy for constructing synthetic biological chassis cells and overcoming obstacles in natural product discovery and production. However, it is of great challenge to discover target genes that can be deleted and optimized due to the complicated genome of actinomycetes. Saccharopolyspora pogona can produce butenyl-spinosyn during aerobic fermentation, and its genome contains 32 different gene clusters. This suggests that there is a large amount of potential competitive metabolism in S. pogona, which affects the biosynthesis of butenyl-spinosyn. By analyzing the genome of S. pogona, six polyketide gene clusters were identified. From those, the complete deletion of clu13, a flaviolin-like gene cluster, generated a high butenyl-spinosyn-producing strain. Production of this strain was 4.06-fold higher than that of the wildtype strain. Transcriptome profiling revealed that butenyl-spinosyn biosynthesis was not primarily induced by the polyketide synthase RppA-like but was related to hypothetical protein Sp1764. However, the repression of sp1764 was not enough to explain the enormous enhancement of butenyl-spinosyn yields in S. pogona-Δclu13. After the comparative proteomic analysis of S. pogona-Δclu13 and S. pogona, two proteins, biotin carboxyl carrier protein (BccA) and response regulator (Reg), were investigated, whose overexpression led to great advantages of butenyl-spinosyn biosynthesis. In this way, we successfully discovered three key genes that obviously optimize the biosynthesis of butenyl-spinosyn. Gene cluster simplification performed in conjunction with multiomics analysis is of great practical significance for screening dominant chassis strains and optimizing secondary metabolism. This work provided an idea about screening key factors and efficient construction of production strains.

Comparative Proteomics Reveals the Effect of the Transcriptional Regulator Sp13016 on Butenyl-Spinosyn Biosynthesis in Saccharopolyspora pogona.

Butenyl-spinosyn is a highly effective and broad-spectrum biopesticide produced by Saccharopolyspora pogona. However, the yield of this compound is difficult to increase because the regulatory mechanism of secondary metabolism is still unknown. Here, the transcriptional regulator Sp13016 was discovered to be highly associated with butenyl-spinosyn synthesis and bacterial growth. Overexpression of sp13016 improved butenyl-spinosyn production to a level that was 2.84-fold that of the original strain, while deletion of sp13016 resulted in a significant decrease in yield and growth inhibition. Comparative proteomics revealed that these phenotypic changes were attributed to the influence of Sp13016 on the central carbon metabolism pathway to regulate the supply of precursors. Our research helps to reveal the regulatory mechanism of butenyl-spinosyn biosynthesis and provides a reference for increasing the yield of natural products of Actinomycetes.

Effects of lytS-L on the primary metabolism and butenyl-spinosyn biosynthesis in Saccharopolyspora pogona.

The LytTR family two-component system widely exists in bacterial cells and plays an important role in metabolic regulation. The lytS-L gene that encodes for a LytTR family sensor kinase was knocked out to study its influence on the growth, phenotype, and the biosynthesis of the insecticidal polyketide butenyl-spinosyn in Saccharopolyspora pogona NRRL 30141 (S. pogona). High performance liquid chromatography (HPLC) results showed that the butenyl-spinosyn yield of the lytS-L knockout mutant decreased by 58.9% compared with that of the parental strain. This is manifested by a weak toxicity of the mutant against the insect Helicoverpa assulta (H. armigera). Comparative proteomic analysis revealed the expression characteristics of the proteins in S. pogona and S. pogona-ΔlytS-L: a total of 14 proteins involved in energy metabolism were down-regulated, 9 proteins related to carbon metabolism such as glycolysis, and tricarboxylic acid cycle (TCA) were up-regulated, while 13 proteins involved in the biosynthesis of butenyl-spinosyn were down-regulated (fold change >1.2 or< 0.83). The qRT-PCR (Quantitative Real-time PCR) analysis illustrated that the changes in the expression levels of transcription and translation of the identified genes were consistent. This study explores the function of the two-component system of the LytTR family in S. pogona and shows that the lytS-L gene has an important influence on regulating primary metabolism and butenyl-spinosyn biosynthesis of S. pogona.

Physical contact, volatiles, and acoustic signals contribute to monogamy in an invasive aggregating bark beetle.

The behavioral strategies and mechanisms by which some insects maintain monogamous mating systems are not well understood. We investigated the mating system of the bark beetle Dendroctonus valens, and identified several contributing mechanisms. Field and laboratory observations suggest the adults commonly form permanent bonds during host colonization. Moreover, it showed mated females that remained paired with males produced more offspring than mated females that were alone in galleries. In bioassays, a second female commonly entered a gallery constructed by a prior female. Videos show she commonly reached the location of the first female, but they did not engage in actual fighting. Rather, the second female typically departs to form her own gallery. Acoustic signaling likewise does not appear to influence female-female encounters, based on controlled muting experiments. Instead, the intruder appears to perceive the resident's presence by physical contact. Both acoustic signals and volatiles released by females during gallery constructing were shown to attract males. After a male joined a female in a gallery, the male-produced aggressive sounds, which were shown by playback to deter other males from entering the gallery. Unlike female-female interactions, resident males use their head and rear to push intruders out of galleries. Additionally, volatiles released by males during feeding repelled intruding males, discouraging them from entering the gallery. Males also construct plugs that block the entrance, which may prevent subsequent males and predators from entering the gallery. Thus, D. valens has evolved multifaceted mechanisms contributing to single pairings that confer benefits to both sexes.

SenX3-RegX3, an Important Two-Component System, Regulates Strain Growth and Butenyl-spinosyn Biosynthesis in Saccharopolyspora pogona.

Butenyl-spinosyn produced by Saccharopolyspora pogona exhibits strong insecticidal activity and a broad pesticidal spectrum. Currently, important functional genes involved in butenyl-spinosyn biosynthesis remain unknown, which leads to difficulty in efficient understanding of its regulatory mechanism and improving its production by metabolic engineering. Here, we present data supporting a role of the SenX3-RegX3 system in regulating the butenyl-spinosyn biosynthesis. EMSAs and qRT-PCR demonstrated that RegX3 positively controls butenyl-spinosyn production in an indirect way. Integrated proteomic and metabolomic analysis, regX3 deletion not only strengthens the basal metabolic ability of S. pogona in the mid-growth phase but also promotes the flow of the acetyl-CoA produced via key metabolic pathways into the TCA cycle rather than the butenyl-spinosyn biosynthetic pathway, which ultimately leads to continued growth but reduced butenyl-spinosyn production. The strategy demonstrated here may be valuable for revealing the regulatory role of the SenX3-RegX3 system in the biosynthesis of other natural products.

RNA-Seq-Based Transcriptomic Analysis of Saccharopolyspora spinosa Revealed the Critical Function of PEP Phosphonomutase in the Replenishment Pathway.

Spinosyns, the secondary metabolites produced by Saccharopolyspora spinosa, are the active ingredients in a family of novel biological insecticides. Although the complete genome sequence of S. spinosa has been published, the transcriptome of S. spinosa remains poorly characterized. In this study, high-throughput RNA sequencing (RNA-seq) technology was applied to dissect the transcriptome of S. spinosa. Through transcriptomic analysis of different periods of S. spinosa growth, we found large numbers of differentially expressed genes and classified them according to their different functions. Based on the RNA-seq data, the CRISPR-Cas9 method was used to knock out the PEP phosphonomutase gene (orf 06952-4171). The yield of spinosyns A and D in S. spinosa-ΔPEP was 178.91 mg/L and 42.72 mg/L, which was 2.14-fold and 1.76-fold higher than that in the wild type (83.51 and 24.34 mg/L), respectively. The analysis of the mutant strains also verified the validity of the transcriptome data. The deletion of the PEP phosphonomutase gene leads to an increase in pyruvate content and affects the biosynthesis of spinosad. The replenishment of phosphoenol pyruvate in S. spinosa provides the substrate for the production of spinosad. We envision that these transcriptomic analysis results will contribute to the further study of secondary metabolites in actinomycetes.