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| 1 | MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle显示文摘Tomato(Solanum lycopersicum)is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research.Although many research efforts have focused on the analysis of metabolite differences between varieties and species,the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie these changes are poorly understood.In this study,we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato tissues and growth stages.In the resulting MicroTom Metabolic Network,the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters based on their biological functions.Using this dataset,we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network.In addition to verifying previously well-established regulatory networks for important metabolites,we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites such as steroidal glycoalkaloids and flavonoids.Our findings provide insights into spatiotemporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants. | Yan Li Yang Chen Lu Zhou Shengjie You Heng Deng Ya Chen Saleh Alseekh Yong Yuan Rao Fu Zixin Zhang Dan Su Alisdair R.Fernie Mondher Bouzayen Tao Ma Mingchun Liu Yang Zhang | 2020 | Molecular Plant2020，13，8： | 10 |
| 2 | A LuxR family transcriptional regulator AniF promotes the production of anisomycin and its derivatives in Streptomyces hygrospinosus var.beijingensis显示文摘The protein synthesis inhibitor anisomycin features a unique benzylpyrrolidine system and exhibits potent selective activity against pathogenic protozoa and fungi.It is one of the important effective components in Agricultural Antibiotic120,which has been widely used as naturally-originated agents for treatment of crop decay in China.The chemical synthesis of anisomycin has recently been reported,but the complex process with low productivity made the biosynthesis still to be a vital mainstay in efforts.The biosynthetic gene cluster(BGC)of anisomycin in Streptomyces hygrospinosus var.beijingensis has been identified in our previous work,while poor understanding of the regulatory mechanism limited the yield enhancement via regulation engineering of S.hygrospinosus var.beijingensis.In this study here,we characterized AniF as an indispensable LuxR family transcriptional regulator for the activation of anisomycin biosynthesis.The genetic manipulations of aniF and the real-time quantitative PCR(RT-qPCR)revealed that it positively regulated the transcription of the anisomycin BGC.Moreover,the overexpression of aniF contributed to the improvement of the production of anisomycin and its derivatives.Dissection of the mechanism underlying the function of AniF revealed that it directly activated the transcription of the genes aniR-G involved in anisomycin biosynthesis.Especially,one AniF-binding site in the promoter region of aniR was identified by DNase I footprinting assay and an inverted repeat sequence(5′-GGGC-3′)composed of two 4-nt half sites in the protected region was found.Taken together,our systematic study confirmed the positive regulatory role of AniF and might facilitate the future construction of engineering strains with high productivity of anisomycin and its derivatives. | Jufang Shen Lingxin Kong Yan Li Xiaoqing Zheng Qing Wang Weinan Yang Zixin Deng Delin You | 2019 | Synthetic and Systems Biotechnology2019，4，1： | 10 |
| 3 | Qualitative analysis of chemical components in Lianhua Qingwen capsule by HPLC-Q Exactive-Orbitrap-MS coupled with GC-MS显示文摘The Lianhua Qingwen(LHQW) capsule is a popular traditional Chinese medicine for the treatment of viral respiratory diseases.In particular,it has been recently prescribed to treat infections caused by the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).However,due to its complex composition,little attention has been directed toward the analysis of chemical constituents present in the LHQW capsule.This study presents a reliable and comprehensive approach to characterizing the chemical constituents present in LHQW by high-performance liquid chromatography-Q Exactive-Orbitrap mass spectrometry(HPLC-Q Exactive-Orbitrap-MS) coupled with gas chromatography-mass spectrometry(GC-MS).An automated library alignment method with a high mass accuracy(within 5 ppm) was used for the rapid identification of compounds.A total of 104 compounds,consisting of alkaloids,flavonoids,phenols,phenolic acids,phenylpropanoids,quinones,terpenoids,and other phytochemicals,were successfully characterized.In addition,the fragmentation pathways and characteristic fragments of some representative compounds were elucidated.GC-MS analysis was conducted to characterize the volatile compounds present in LHQW.In total,17 compounds were putatively characterized by comparing the acquired data with that from the NIST library.The major constituent was menthol,and all the other compounds were terpenoids.This is the first comprehensive report on the identification of the major chemical constituents present in the LHQW capsule by HPLC-Q Exactive-Orbitrap-MS,coupled with GCMS,and the results of this study can be used for the quality control and standardization of LHQW capsules. | Shuai Fu Rongrong Cheng Zixin Deng Tiangang Liu | 2021 | Journal of Pharmaceutical Analysis2021，11，6： | 8 |
| 4 | Structural insights into DndE from Escherichia coil B7A involved in DNA phosphorothioation modification显示文摘 | Wei Hu Chengkun Wang Jingdan Liang Tianlong Zhang Zhongpei Hu Zhijun Wang Wenxian Lan Fang Li Houming Wu Jianping Ding Geng Wu Zixin Deng Chunyang Cao | 2012 | Cell Research2012，22，7： | 7 |
| 5 | Heterologous expression of Avermectins biosynthetic gene cluster by construction of a Bacterial Artificial Chromosome library of the producers显示文摘Avermectins,a group of polyketide natural products,are widely used as anthelmintics in agriculture.Metabolic engineering and combinatorial biosynthesis were extensively employed to improve Avermectins production and create novel Avermectin derivatives,including Ivermectin and Doramectin.It is labor intensive and time cost to genetically manipulate Avermectins producer Streptomyces avermitilis in vivo.Cloning and heterologous expression of Avermectins biosynthetic gene cluster will make it possible to tailor the cluster in vitro.We constructed a Bacterial Artificial Chromosome(BAC)library of S.avermitilis ATCC 31267 with inserted DNA fragments ranged from 100 to 130 Kb.Five recombinant BAC clones which carried the Avermectins biosynthetic gene cluster ave(81 Kb in size)were screened out from the library.Then,ave was hetero-expressed in S.lividans.Three Avermectin components,A2a,B1a and A1a were detected from the cell extracts of recombinant strains.It will facilitate the development of Avermectin derivatives by polyketide synthase domain swapping and provide functional element for Avermectins synthetic biology study. | Qian Deng Li Zhou Meizhong Luo Zixin Deng Changming Zhao | 2017 | Synthetic and Systems Biotechnology2017，2，1： | 5 |
| 6 | Inactivation of the positive LuxR-type oligomycin biosynthesis regulators OlmRI and OlmRII increases avermectin production in Streptomyces avermitilis显示文摘Oligomycins are a group of 26 macrocyclic lactones that exhibit broad biological activities,including antifungal,anticancer and nematocidal activities.Analysis of the oligomycin biosynthetic gene cluster (olm) in S.avermitilis revealed 2 tandem LuxR-type regulators,OlmRI (931 aa) and OlmRII (941 aa),with shared identity of 38%.Gene replacement of olmRI or olmRII abolished oligomycin production,and this production could be partially restored in the disruptants by introducing cloned olmRI and olmRII with their native promoters,demonstrating the essential role of OlmRI and OlmRII for oligomycin biosynthesis.Quantitative real-time RT-PCR analysis revealed that transcription of 14 olm genes was differentially affected by the deletion of olmRI and olmRII.Unexpectedly,avermectin production in both mutants was enhanced at least 4-fold.The identification of the positive cluster-situated regulators,OlmRI and OlmRII,paves the way for the transcriptional analysis of oligomycin biosynthesis and for the enhancement of oligomycin and avermectin production through regulator engineering. | YU Qing BAI LinQuan ZHOU XiuFen DENG ZiXin | 2012 | Chinese Science Bulletin2012，57，8： | 4 |
| 7 | Asm8, a specific LAL-type activator of 3-amino-5-hydroxy-benzoate biosynthesis in ansamitocin production显示文摘The highly potent antitumor agent ansamitocin P3 is a macrolactam isolated from Actinosynnema pretiosum ATCC 31565. A 120-kb DNA fragment was previously identified as the ansamitocin biosynthetic gene cluster, and contains genes for polyketide assembly, precursor synthesis, post-polyketide synthesis modification, and regulation. Within the biosynthetic gene cluster, asm8 encodes an 1117-amino-acid protein with a high degree of similarity to the large ATP-binding LuxR family-type regulators. In the current study, we determined that inactivation of asm8 by gene replacement in ATCC 31565 resulted in the complete loss of ansamitocin production, and that complementation with a cloned asm8 gene restored ansamitocin biosynthesis. Interestingly, the disruption of asm8 decreased the transcription of genes responsible for 3-amino-5-hydroxybenzoate (AHBA) formation, the starter unit required for ansamitocin biosynthesis. Subsequently, feeding of exogenous AHBA to the asm8 mutant restored ansamitocin biosynthesis, which showed that Asm8 is a specific positive regulator in AHBA biosynthesis. In addition, investigation of asm8 homologs identified two new ansamitocin producers, and inactivation of the asm8 homolog in A. pretiosum ATCC 31280 abolished ansamitocin production in this strain. Characterization of the positive regulator Asm8 and discovery of the two new ansamitocin producers paves the way for further improving production of this important antitumor agent. | PAN WenQin KANG QianJin WANG Lei BAI LinQuan DENG ZiXin | 2013 | Science China(Life Sciences)2013，56，7： | 4 |
| 8 | Characterization of the positive SARP family regulator PieR for improving piericidin A1 production in Streptomyces piomogeues var.Hangzhouwanensis显示文摘Piericidin A1,a member ofɑ-pyridone antibiotic,exhibits various biological activities such as antimicrobial,antifungal,and antitumor properties and possesses potent respiration-inhibitory activity against insects due to its competitive binding capacity to mitochondrial complex I.The biosynthetic pathway of piericidin A1 has been reported in Streptomyces piomogeues var.Hangzhouwanensis,while the regulatory mechanism remains poorly understood.In this study,a Streptomyces antibiotic regulatory protein(SARP)family transcriptional regulator PieR was characterized.Genetic disruption and complementation manipulations revealed that PieR positively regulated the production of piericidin A1.Moreover,the overexpression of pieR contributed to the improvement of piericidin A1 productivity.The real-time quantitative PCR(RT-qPCR)was carried out and the data showed that pieR stimulated the transcription of all the biosynthesis-related genes for piericidin A1.In order to explore the regulatory mechanism,electrophoresis mobility shift assays(EMSA)and DNase I footprinting experiments have been conducted.A protected region covering 50 nucleotides within the upstream region of pieR was identified and two 5-nt direct repeat sequences(5′-CCGGA-3′)in the protected region were found.These findings,taken together,set stage for transcriptional control engineering in the view of optimizing piericidin A1 production and thus provide a viable potent route for the construction of strains with high productivity. | Yan Li Lingxin Kong Jufang Shen Qing Wang Qian Liu Weinan Yang Zixin Deng Delin You | 2019 | Synthetic and Systems Biotechnology2019，4，1： | 4 |
| 9 | Streptomyces avermitilis industrial strain as cell factory for Ivermectin B1a production显示文摘Ivermectin,a kind of valuable derivatives of Avermectin,is distinct from Avermectin due to the saturated bond at C22eC23 position.Combinatorial biosynthesis of Ivermectins based on Avermectins biosynthetic gene cluster(ave)has been achieved recently,while the establishment of an Ivermectin homogeneous component producing strain is challenging because of the limited compatibility between the native and heterologous polyketide synthase(PKS)domains.In this study,the PKS module 2 Dehydratase(DH)-Enoylreductase(ER)-Ketoreductase(KR)domain set of Meilingmycin,which is another naturally occurring homologue of Avermectin,was employed to substitute the DH-KR domains of Avermectins PKS module 2 to generate an Ivermectin biosynthetic gene cluster(ive).Ivermectins B1a and A1a were heterologously biosynthesized in a classic actinomyces host Streptomyces lividans.The Avermectin B1a high-producing strain S.avermitilis 3-115 was genetically engineered to give an artificial host cell and Ivermectin B1a single component was effectively produced with a production of 1.25±0.14 g/L. | Qian Deng Liqiongzi Xiao Yang Liu Lixin Zhang Zixin Deng Changming Zhao | 2019 | Synthetic and Systems Biotechnology2019，4，1： | 3 |
| 10 | Puromycin A, B and C, cryptic nucleosides identified from Streptomyces alboniger NRRL B-1832 by PPtase-based activation显示文摘Natural product discovery is pivot for drug development,however,this endeavor is often challenged by the wide inactivation or silence of natural products biosynthetic pathways.We recently developed a highly efficient approach to activate cryptic/silenced biosynthetic pathways through augmentation of the phosphopantetheinylation of carrier proteins.By applying this approach in the Streptomyces alboniger NRRL B-1832,we herein identified three cryptic nucleosides products,including one known puromycin A and two new derivatives(puromycin B and C).The biosynthesis of these products doesn't require the involvement of carrier protein,indicating the phosphopantetheinyl transferase(PPtase)indeed plays a fundamental regulatory role in metabolites biosynthesis.These results demonstrate that the PPtasebased approach have a much broader effective scope than the previously assumed carrier proteininvolving pathways,which will benefit future natural products discovery and biosynthetic studies. | Xiaoli Yan Benyin Zhang Wenya Tian Qi Dai Xiaoqin Zheng Ke Hu Xinxin Liu Zixin Deng Xudong Qu | 2018 | Synthetic and Systems Biotechnology2018，3，1： | 3 |
| 11 | In vitro reconstitution guide for targeted synthetic metabolism of chemicals, nutraceuticals and drug precursors显示文摘With the developments in metabolic engineering and the emergence of synthetic biology,many breakthroughs in medicinal,biological and chemical products as well as biofuels have been achieved in recent decades.As an important barrier to traditional metabolic engineering,however,the identification of ratelimiting step(s)for the improvement of specific cellular functions is often difficult.Meanwhile,in the case of synthetic biology,more and more BioBricks could be constructed for targeted purposes,but the optimized assembly or engineering of these components for high-efficiency cell factories is still a challenge.Owing to the lack of steady-state kinetic data for overall flux,balancing many multistep biosynthetic pathways is time-consuming and needs vast resources of labor and materials.A strategy called targeted engineering is proposed in an effort to solve this problem.Briefly,a targeted biosynthetic pathway is to be reconstituted in vitro and then the contribution of cofactors,substrates and each enzyme will be analyzed systematically.Next is in vivo engineering or de novo pathway assembly with the guidance of information gained from in vitro assays.To demonstrate its practical application,biosynthesis pathways for the production of important products,e.g.chemicals,nutraceuticals and drug precursors,have been engineered in Escherichia coli and Saccharomyces cerevisiae.These cases can be regarded as concept proofs indicating targeted engineering might help to create high-efficiency cell factories based upon constructed biological components. | Gao-Yi Tan Faying Zhu Zixin Deng Tiangang Liu | 2016 | Synthetic and Systems Biotechnology2016，1，1： | 3 |
| 12 | Indole methylation protects diketopiperazine configuration in the maremycin biosynthetic pathway显示文摘The maremycin biosynthetic gene cluster has been identified in Streptomyces sp. B9173. Comparative metabolic profiling with knockout mutant strains led to the identification of new products correlated to the maremycin biosynthesis, in particular the'demethyl'-maremycins with an unexpected D-tryptophan unit. A biosynthetic pathway for the maremycins is proposed and plausible reasoning for tryptophan epimerization in the demethylmaremycin biosynthesis is also provided. | Yingxia Lan Yi Zou Tingting Huang Xiaozheng Wang Nelson L. Brock Zixin Deng Shuangjun Lin | 2016 | Science China Chemistry2016，59，9： | 3 |
| 13 | Biosynthesis of tetronate antibiotics:A growing family of natural products with broad biological activities显示文摘Tetronate antibiotics,a growing family of natural products featuring a characteristic tetronic acid moiety,are of importance and of particular interest for their typical structures,especially the spirotetronate structure,and corresponding versatile biological activities.Considerable efforts have persistently performed since the first tetronate was isolated,to elucidate the biosynthesis of natural tetronate products,by isotope-labeled feeding experiments,genetical characterization of biosynthetic gene clusters,and biochemical reconstitution of key enzymatic catalyzed reactions.Accordingly,the biosynthesis of spirotetronates has been gradually determined,including biosynthesis of a polyketide-derived backbone for spirotetronate aglycone,incorporation of a glycerol-derived three-carbon unit into tetronic acid moiety,formation of mature aglycone via Diels-Alder-like reaction,and decorations of aglycone with various deoxysugar moieties.In this paper,the biosynthetic investigations of natural tetronates are well documented and a common biosynthetic route for this group of natural products is summarized accordingly. | TAO WeiXin ZHU MangHong DENG ZiXin SUN YuHui | 2013 | Science China Chemistry2013，56，10： | 3 |
| 14 | Translational Genomics to Develop a Salmonella enterica Serovar Paratyphi A Multiplex Polymerase Chain Reaction Assay显示文摘 | Hong-Yu Ou Cindy Teh Shuan Ju Kwai-Lin Thong Norazah Ahmad Zixin Deng Michael R. Barer Kumar Rajakumar | 2007 | The Journal of Molecular Diagnostics2007，，5： | 2 |
| 15 | Twenty years hunting for sulfur in DNA显示文摘Here we tell a 20-year long story.It began with an easily overlooked DNA degradation(Dnd)phenomenon during electrophoresis and eventually led to the discovery of an unprecedented DNA sulfur modification governed by five dnd genes.This unusual DNA modification,called phosphorothioation,is the first physiological modification identified on the DNA backbone,in which the nonbridging oxygen is replaced by sulfur in a sequence selective and stereo-specific manner.Homologous dnd gene clusters have been identified in diverse and distantly related bacteria and thus have drawn immediate attention of the entire microbial scientific community.Here,we summarize the progress in chemical,genetic,enzymatic,bioinformatical and analytical aspects of this novel postreplicative DNA modification.We also discuss perspectives on the physiological functions of the DNA phosphorothioate modification in bacteria and their implications. | Shi Chen Lianrong Wang Zixin Deng | 2010 | Protein & Cell2010，1，1： | 2 |
| 16 | A Practical Process for the Synthesis of Translocator Protein 18kDa Imidazopyridine Ligand显示文摘In this article, an effective feasible method to synthesize translocator protein 18kDa(TSPO) imidazopyridine ligand 7 is discussed. A new procedure for the synthesis of the key intermediate 17 has been developed in four steps(condensation, diazo reaction, hydrolysis, amidation) from 2-aminopyridine 18. The overall yield was increased from 18% to 31.6%. One of the key steps is using activated copper powder as a catalyst in several cycles. Finally, reduction of 17 with Zn dust completed the synthesis of TSPO imidazopyridine ligand 7 in 86% yield. | WEN Meng QU Chunrong SU Xinhui DING Mingmin DENG Zixin HONG Xuechuan | 2014 | Wuhan University Journal of Natural Sciences2014，19，1： | 2 |
| 17 | Revolution of vitamin E production by starting from microbial fermented farnesene to isophytol显示文摘Vitamin E is one of the most widely used vitamins.In the classical commercial synthesis of vitamin E(a-tocopherol),the chemical synthesis of isophytol is the key technical barrier.Here,we establish a new process for isophytol synthesis from microbial fermented farnesene.To achieve an efficient pathway for farnesene production,Saccharomyces cerevisiae was selected as the host strain.First,b-farnesene synthase genes from different sources were screened,and through protein engineering and system metabolic engineering. | Ziling Ye Bin Shi Yanglei Huang Tian Ma Zilei Xiang Ben Hu Zhaolin Kuang Man Huang Xiaoying Lin Zhu Tian Zixin Deng Kun Shen Tiangang Liu | 2022 | The Innovation2022，3，3： | 2 |
| 18 | SynBioEcoli: a comprehensive metabolism network of engineered E. coil in three dimensional visualization显示文摘设计 E 的一个全面新陈代谢网络。coli 在系统生物学是很重要的, metabolomics 学习。许多工具集中于二维的空格在新陈代谢的网络显示小径。然而,三维的可视化的用法可以帮助更好理解新陈代谢、规章的网络的复杂拓扑学。方法我们手工地从文学的大量试验性的数据(包括的小径,反应和代谢物) 与设计 E 的不同类型联系了的 curated。coli 然后利用了三维的可视化的一种新奇技术开发一个全面新陈代谢的网络命名 SynBioEcoli。结果 SynBioEoli 包含 740 条 biosynthetic 小径, 3,889 新陈代谢的反应, 2,255 化学药品手工地从与设计 E 的不同类型联系的大约 11,000 份新陈代谢出版物加重 curated。coli。而且, SynBioEcoli 与各种各样的信息科学技术集成。结论 SynBioEcoli 能被认为是设计 E 的全面 knowledgebase。coli 并且代表下一代细胞的新陈代谢网络可视化技术。它能经由浏览器被存取(例如 Google 铬) 支持 WebGL,在 http://gffzz849681930f04473ch59k6oof09co06nxk.ffgz.tsg.suse.edu.cn/synbioecoli/ 。 | Weizhong Tu Shaozhen Ding Ling Wu Zhe Deng Hui Zhu Xiaotong Xu Chen Lin Chaonan Ye Minlu Han Mengna Zhao Juan Liu Zixin Deng Junni Chen Dong-Qing Wei Qian-Nan Hu | 2017 | Frontiers of Electrical and Electronic Engineering in China2017，5，1： | 2 |
| 19 | An unusual UMP C-5 methylase in nucleoside antibiotic polyoxin biosynthesis显示文摘 | Wenqing Chen Yan Li Jie Li Lian Wu Renxiao Wang Zixin Deng Jiahai Zhou | 2016 | Protein & Cell2016，7，9： | 2 |
| 20 | Efficient editing DNA regions with high sequence identity in actinomycetal genomes by a CRISPR-Cas9 system显示文摘Actinobacteria able to produce varieties of bioactive natural products have been long appreciated by the field of drug discovery and development.Recently,a few of CRISPR/Cas9 systems bearing different types of replicons(pSG5 and pIJ101)were developed to efficiently edit their genomes.Despite wide application in gene editing,their utility in editing challenging DNA regions e.g.high sequence identity has not been compared.In this study,we confirmed that the widely used temperature-sensitive pSG5 replicon is indeed not suitable for editing modular polyketide synthase(PKS)genes due to causing unpredicted gene recombination.This problem can be addressed by replacing the pSG5 with the segregationally unstable pIJ101 replicon.By introducing a counterselection marker CodA,convenient cloning sites in the single guide RNAs(sgRNAs)and homologous template scaffolds,we developed a new CRISPR-Cas9 system pMWCas9.This system was successfully used to delete/replace erythromycin PKS and other biosynthetic genes in Saccharopolyspora erythraea and Streptomyces sp.AL2110.By swapping the promoters of antB and antC with ermE and kasOp,we achieved a deacyl-antimycin hyper producer which produces a 9-fold higher yield than the original Streptomyces sp.AL2110 strain.Our results provide a robust and useful Cas9 tool for genetic studies in Actinobacteria. | Jingjun Mo Shuwen Wang Wan Zhang Chunyu Li Zixin Deng Lixin Zhang Xudong Qu | 2019 | Synthetic and Systems Biotechnology2019，4，2： | 2 |
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