Taxus,commonly known as yew,is a well-known gymnosperm with great ornamental and medicinal value.In this study,by assembling a chromosome-level genome of the Himalayan yew(Taxus wallichiana)with 10.9 Gb in 12 chromoso...Taxus,commonly known as yew,is a well-known gymnosperm with great ornamental and medicinal value.In this study,by assembling a chromosome-level genome of the Himalayan yew(Taxus wallichiana)with 10.9 Gb in 12 chromosomes,we revealed that tandem duplication acts as the driving force of gene family evolution in the yew genome,resulting in the main genes for paclitaxel biosynthesis,i.e.those encoding the taxadiene synthase,P450s,and transferases,being clustered on the same chromosome.The tandem duplication may also provide genetic resources for the nature to sculpt the core structure of taxoids at different positions and subsequently establish the complex pathway of paclitaxel by neofunctionalization.Furthermore,we confirmed that there are two genes in the cluster encoding isoenzymes of a known enzyme in the paclitaxel biosynthetic pathway.The reference genome of the Himalayan yew will serve as a platform for decoding the complete biosynthetic pathway of paclitaxel and understanding the chemodi-versity of taxoids in gymnosperms.展开更多
The aim of our study was to assess differences in the expression of genes involved in fruit softening and ethylene biosynthetic pathways under different temperature storage conditions. Different peach cultivars of ‘X...The aim of our study was to assess differences in the expression of genes involved in fruit softening and ethylene biosynthetic pathways under different temperature storage conditions. Different peach cultivars of ‘Xiacui' and ‘Yumyeong', which are stonyhard, ‘Yinhualu', which is softmelting, ‘Hujing Milu', which is hard-melting, and ‘Baby Gold 6', which is non-melting at 80% ripening, were collected as test materials. The results showed that only slight ethylene production was detected after harvesting of ‘Yumyeong' and ‘Xiacui' under either a room temperature(25 °C) or low temperature(4 °C). The fruit firmness of stonyhard cultivars was retained at a high level under room temperature over time, whereas a low temperature induced ‘Yumyeong' fruit to soften. Quantitative real-time PCR results indicated that the PpACS1 gene was highly expressed in soft-melting, hard-melting and non-melting cultivars; however, expression was extremely low in stonyhard peaches. PpACS2 or PpACS3, however,was not detected in all five cultivars. Interestingly, cold treatment significantly decreased firmness along with endo-PG expression obviously upregulated in ‘Yumyeong', but not in ‘Xiacui' peaches. In conclusion, this study revealed that fruit softening of peaches with different flesh textures was closely related to ethylene biosynthesis during the storage period, which was controlled via regulating relevant gene expression levels under different storage temperatures.展开更多
In order to enhance berry coloration of bright-red grape cultivars, the effects of abscisic acid (ABA) treatment on the quantity and composition of anthocyanins as well as the expression of genes related to flavonoid ...In order to enhance berry coloration of bright-red grape cultivars, the effects of abscisic acid (ABA) treatment on the quantity and composition of anthocyanins as well as the expression of genes related to flavonoid biosynthesis in the berry were examined. Exogenous ABA treatment increased anthocyanin content, especially petunidin- and malvidin-type anthocyanins. Quantitative real-time PCR analysis revealed that ABA treatment around véraison resulted in the upregulation of genes encoding enzymes responsible for both general flavonoid and anthocyanin biosynthesis. On the other hand, the gene expressions of enzymes involved in proanthocyanidin synthesis were drastically decreased at véraison and remained extremely low even with ABA treatment. Thus, increases in the total amount and composition ratios of petunidin- and malvidin-type anthocyanins were mainly caused by ABA-induced upregulation of uridine diphosphate glucose flavonoid glucosyl transferase, glutathione S-transferase 4, O-methyl transferase and flavonoid 3’, 5’ hydroxylase expression, resulting in the deep coloration of berry of skin.展开更多
Biosynthetic gene clusters(BGCs)are regions of a genome where genes involved in a biosynthetic pathway are in proximity.The origin and evolution of plant BGCs as well as their role in specialized metabolism remain lar...Biosynthetic gene clusters(BGCs)are regions of a genome where genes involved in a biosynthetic pathway are in proximity.The origin and evolution of plant BGCs as well as their role in specialized metabolism remain largely unclear.In this study,we have assembled a chromosome-scale genome of Japanese catnip(Schizonepeta tenuifolia)and discovered a BGC that contains multiple copies of genes involved in four adjacent steps in the biosynthesis of p-menthane monoterpenoids.This BGC has an unprecedented bipartite structure,with mirrored biosynthetic regions separated by 260 kilobases.This bipartite BGC includes identical copies of a gene encoding an old yellow enzyme,a type of flavin-dependent reductase.In vitro assays and virus-induced gene silencing revealed that this gene encodes the missing isopiperitenone reductase.This enzyme evolved from a completely different enzyme family to isopiperitenone reductase from closely related Mentha spp.,indicating convergent evolution of this pathway step.Phylogenomic analysis revealed that this bipartite BGC has emerged uniquely in the S.tenuifolia lineage and through insertion of pathway genes into a region rich in monoterpene synthases.The cluster gained its bipartite structure via an inverted duplication.The discovered bipartite BGC for p-menthane biosynthesis in S.tenuifolia has similarities to the recently described duplicated p-menthane biosynthesis gene pairs in the Mentha longifolia genome,providing an example of the convergent evolution of gene order.This work expands our understanding of plant BGCs with respect to both form and evolution,and highlights the power of BGCs for gene discovery in plant biosynthetic pathways.展开更多
Pristinamycin,produced by Streptomyces pristinaespiralis,which is a streptogramin-like antibiotic consisting of two chemically unrelated components:pristinamycin I(PI)and pristinamycin II(PII),shows potent activity ag...Pristinamycin,produced by Streptomyces pristinaespiralis,which is a streptogramin-like antibiotic consisting of two chemically unrelated components:pristinamycin I(PI)and pristinamycin II(PII),shows potent activity against many antibiotic-resistant pathogens.However,so far pristinamycin production titers are still quite low,particularly those of PI.In this study,we constructed a PI single component producing strain by deleting the PII biosynthetic genes(snaE1 and snaE2).Then,two metabolic engineering approaches,including deletion of the repressor gene papR3 and chromosomal integration of an extra copy of the PI biosynthetic gene cluster(BGC),were employed to improve PI production.The final engineered strain DPIIDpapR3/PI produced a maximum PI level of 132 mg/L,with an approximately 2.4-fold higher than that of the parental strain S.pristinaespiralis HCCB10218.Considering that the PI biosynthetic genes are clustered in two main regions in the 210 kb“supercluster”containing the PI and PII biosynthetic genes as well as a cryptic polyketide BGC,these two regions were cloned separately and then were successfully assembled into the PI BGC by the transformation-associated recombination(TAR)system.Collectively,the metabolic engineering approaches employed is very efficient for strain improvement in order to enhance PI titer.展开更多
Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(AR...Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments.To address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based methodology.Our findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical conditions.We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel antibiotics.Our study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.展开更多
A 61-kb biosynthetic gene cluster(BGC),which is accountable for the biosynthesis of hibarimicin(HBM)B from Microbispora rosea subsp.hibaria TP-A0121,was heterologously expressed in Streptomyces coelicolor M1154,which ...A 61-kb biosynthetic gene cluster(BGC),which is accountable for the biosynthesis of hibarimicin(HBM)B from Microbispora rosea subsp.hibaria TP-A0121,was heterologously expressed in Streptomyces coelicolor M1154,which generated a trace of the target products but accumulated a large amount of shunt products.Based on rational analysis of the relevant secondary metabolism,directed engineering of the biosynthetic pathways resulted in the high production of HBM B,as well as new HBM derivates with improved antitumor activity.These results not only establish a biosynthetic system to effectively synthesize HBMs-a class of the largest and most complex Type-Ⅱpolyketides,with a unique pseudo-dimeric structure-but also set the stage for further engineering and deep investigation of this complex biosynthetic pathway toward potent anticancer drugs.展开更多
基金the National Key R&D Program of China(2020YFA0908000)National Science Fund for Excellent Young Scholars(31922047)+1 种基金Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project(No.TSBICIP-KJGG-002)the China Postdoctoral Science Foundation(No.2019M661032)。
文摘Taxus,commonly known as yew,is a well-known gymnosperm with great ornamental and medicinal value.In this study,by assembling a chromosome-level genome of the Himalayan yew(Taxus wallichiana)with 10.9 Gb in 12 chromosomes,we revealed that tandem duplication acts as the driving force of gene family evolution in the yew genome,resulting in the main genes for paclitaxel biosynthesis,i.e.those encoding the taxadiene synthase,P450s,and transferases,being clustered on the same chromosome.The tandem duplication may also provide genetic resources for the nature to sculpt the core structure of taxoids at different positions and subsequently establish the complex pathway of paclitaxel by neofunctionalization.Furthermore,we confirmed that there are two genes in the cluster encoding isoenzymes of a known enzyme in the paclitaxel biosynthetic pathway.The reference genome of the Himalayan yew will serve as a platform for decoding the complete biosynthetic pathway of paclitaxel and understanding the chemodi-versity of taxoids in gymnosperms.
基金supported by the Jiangsu Agriculture Science and Technology Innovation Fund[CX(14)2015]China Agriculture Research System(CARS-31)
文摘The aim of our study was to assess differences in the expression of genes involved in fruit softening and ethylene biosynthetic pathways under different temperature storage conditions. Different peach cultivars of ‘Xiacui' and ‘Yumyeong', which are stonyhard, ‘Yinhualu', which is softmelting, ‘Hujing Milu', which is hard-melting, and ‘Baby Gold 6', which is non-melting at 80% ripening, were collected as test materials. The results showed that only slight ethylene production was detected after harvesting of ‘Yumyeong' and ‘Xiacui' under either a room temperature(25 °C) or low temperature(4 °C). The fruit firmness of stonyhard cultivars was retained at a high level under room temperature over time, whereas a low temperature induced ‘Yumyeong' fruit to soften. Quantitative real-time PCR results indicated that the PpACS1 gene was highly expressed in soft-melting, hard-melting and non-melting cultivars; however, expression was extremely low in stonyhard peaches. PpACS2 or PpACS3, however,was not detected in all five cultivars. Interestingly, cold treatment significantly decreased firmness along with endo-PG expression obviously upregulated in ‘Yumyeong', but not in ‘Xiacui' peaches. In conclusion, this study revealed that fruit softening of peaches with different flesh textures was closely related to ethylene biosynthesis during the storage period, which was controlled via regulating relevant gene expression levels under different storage temperatures.
文摘In order to enhance berry coloration of bright-red grape cultivars, the effects of abscisic acid (ABA) treatment on the quantity and composition of anthocyanins as well as the expression of genes related to flavonoid biosynthesis in the berry were examined. Exogenous ABA treatment increased anthocyanin content, especially petunidin- and malvidin-type anthocyanins. Quantitative real-time PCR analysis revealed that ABA treatment around véraison resulted in the upregulation of genes encoding enzymes responsible for both general flavonoid and anthocyanin biosynthesis. On the other hand, the gene expressions of enzymes involved in proanthocyanidin synthesis were drastically decreased at véraison and remained extremely low even with ABA treatment. Thus, increases in the total amount and composition ratios of petunidin- and malvidin-type anthocyanins were mainly caused by ABA-induced upregulation of uridine diphosphate glucose flavonoid glucosyl transferase, glutathione S-transferase 4, O-methyl transferase and flavonoid 3’, 5’ hydroxylase expression, resulting in the deep coloration of berry of skin.
基金supported by the National Natural Science Foundation of China(grant nos.81973435 and 81473313)the National Natural Science Foundation for Young Scientists of China(grant no.81903756)+2 种基金the Open Project of the Natural Science Foundation of Nanjing University of Chinese Medicine(no.NZY81903756)research on ecological planting and quality assurance of Jiangsu Dao-di herbs(2021)and a Jiangsu Government Scholarship for Overseas Studies(JS-2020-044).We also acknowledge support from the BBSRC(BBN006452/1)and UKRI(MR/S01862X/1).
文摘Biosynthetic gene clusters(BGCs)are regions of a genome where genes involved in a biosynthetic pathway are in proximity.The origin and evolution of plant BGCs as well as their role in specialized metabolism remain largely unclear.In this study,we have assembled a chromosome-scale genome of Japanese catnip(Schizonepeta tenuifolia)and discovered a BGC that contains multiple copies of genes involved in four adjacent steps in the biosynthesis of p-menthane monoterpenoids.This BGC has an unprecedented bipartite structure,with mirrored biosynthetic regions separated by 260 kilobases.This bipartite BGC includes identical copies of a gene encoding an old yellow enzyme,a type of flavin-dependent reductase.In vitro assays and virus-induced gene silencing revealed that this gene encodes the missing isopiperitenone reductase.This enzyme evolved from a completely different enzyme family to isopiperitenone reductase from closely related Mentha spp.,indicating convergent evolution of this pathway step.Phylogenomic analysis revealed that this bipartite BGC has emerged uniquely in the S.tenuifolia lineage and through insertion of pathway genes into a region rich in monoterpene synthases.The cluster gained its bipartite structure via an inverted duplication.The discovered bipartite BGC for p-menthane biosynthesis in S.tenuifolia has similarities to the recently described duplicated p-menthane biosynthesis gene pairs in the Mentha longifolia genome,providing an example of the convergent evolution of gene order.This work expands our understanding of plant BGCs with respect to both form and evolution,and highlights the power of BGCs for gene discovery in plant biosynthetic pathways.
基金This work was sponsored by the National Natural Science Foundation of China(31430004,31421061,31630003,31370081 and 31570072)the Science and Technology Commission of Shanghai Municipality(16490712100).
文摘Pristinamycin,produced by Streptomyces pristinaespiralis,which is a streptogramin-like antibiotic consisting of two chemically unrelated components:pristinamycin I(PI)and pristinamycin II(PII),shows potent activity against many antibiotic-resistant pathogens.However,so far pristinamycin production titers are still quite low,particularly those of PI.In this study,we constructed a PI single component producing strain by deleting the PII biosynthetic genes(snaE1 and snaE2).Then,two metabolic engineering approaches,including deletion of the repressor gene papR3 and chromosomal integration of an extra copy of the PI biosynthetic gene cluster(BGC),were employed to improve PI production.The final engineered strain DPIIDpapR3/PI produced a maximum PI level of 132 mg/L,with an approximately 2.4-fold higher than that of the parental strain S.pristinaespiralis HCCB10218.Considering that the PI biosynthetic genes are clustered in two main regions in the 210 kb“supercluster”containing the PI and PII biosynthetic genes as well as a cryptic polyketide BGC,these two regions were cloned separately and then were successfully assembled into the PI BGC by the transformation-associated recombination(TAR)system.Collectively,the metabolic engineering approaches employed is very efficient for strain improvement in order to enhance PI titer.
基金supported by the National Key Research and Development Program of China(2023YFC2706503)the National Natural Science Foundation of China(32370720)+9 种基金Beihang University&Capital Medical University Plan(BHME-201904)the Open Research Fund of Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE,ECNU,Key Laboratory of MEA,Ministry of Education,ECNU,Key Laboratory of Ecology and Energy Saving Study of Dense Habitat(Tongji University),Ministry of Education-Shanghai Tongji Urban Planning&Design Institute Co.,Ltd Joint Research Project(KY-2022-LH-A03)Shanghai Tongji Urban Planning&Design Institute Co.,Ltd-China Intelligent Urbanization Co-creation Center for High Density Region Research Project(KY-2022-PT-A02)the Irma T.Hirschl and Monique Weill-Caulier Charitable TrustsBert L and N Kuggie Vallee Foundationthe World Quant FoundationThe Pershing Square Sohn Cancer Research Alliancethe National Institutes of Health(R01AI151059)the National Science Foundation(1840275)the Alfred P.Sloan Foundation(G-2015-13964)。
文摘Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments.To address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based methodology.Our findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical conditions.We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel antibiotics.Our study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.
基金supported in part by grants from the National Key Research and Development Program of China(2018YFA0901900)the National Natural Science Foundation of China(22137009)the China Postdoctoral Science Foundation(2020M671271).
文摘A 61-kb biosynthetic gene cluster(BGC),which is accountable for the biosynthesis of hibarimicin(HBM)B from Microbispora rosea subsp.hibaria TP-A0121,was heterologously expressed in Streptomyces coelicolor M1154,which generated a trace of the target products but accumulated a large amount of shunt products.Based on rational analysis of the relevant secondary metabolism,directed engineering of the biosynthetic pathways resulted in the high production of HBM B,as well as new HBM derivates with improved antitumor activity.These results not only establish a biosynthetic system to effectively synthesize HBMs-a class of the largest and most complex Type-Ⅱpolyketides,with a unique pseudo-dimeric structure-but also set the stage for further engineering and deep investigation of this complex biosynthetic pathway toward potent anticancer drugs.
