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Synthetic and Systems Biotechnology

Lorna Suckling, Ciaran McFarlane, Chelsea Sawyer, Stephen P Chambers, Richard I Kitney, David W McClymont, Paul S Freemont
High-throughput preparation of plasmid DNA libraries for next-generation sequencing (NGS) is an important capability for molecular biology laboratories. In particular, it is an essential quality control (QC) check when large numbers of plasmid variants are being generated. Here, we describe the use of the Design of Experiments (DOE) methodology to optimise the miniaturised preparation of plasmid DNA libraries for NGS, using the Illumina® Nextera XT technology and the Labcyte Echo® acoustic liquid dispensing system...
March 2019: Synthetic and Systems Biotechnology
Huixin Xie, Qinqin Zhao, Xin Zhang, Qianjin Kang, Linquan Bai
The α-glucosidase inhibitor acarbose is produced in large-scale by strains derived from Actinoplanes sp. SE50 and used widely for the treatment of type-2 diabetes. Compared with the wild-type SE50, a high-yield derivative Actinoplanes sp. SE50/110 shows 2-fold and 3-7-fold improvement of acarbose yield and acb cluster transcription, respectively. The genome of SE50 was fully sequenced and compared with that of SE50/110, and 11 SNVs and 4 InDels, affecting 8 CDSs, were identified in SE50/110. The 8 CDSs were individually inactivated in SE50...
March 2019: Synthetic and Systems Biotechnology
Jufang Shen, Lingxin Kong, Yan Li, Xiaoqing Zheng, Qing Wang, Weinan Yang, Zixin Deng, Delin You
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...
March 2019: Synthetic and Systems Biotechnology
Qian Deng, Liqiongzi Xiao, Yang Liu, Lixin Zhang, Zixin Deng, Changming Zhao
Ivermectin, a kind of valuable derivatives of Avermectin, is distinct from Avermectin due to the saturated bond at C22-C23 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 )...
March 2019: Synthetic and Systems Biotechnology
Haotian Chi, Xiaoli Wang, Yue Shao, Ying Qin, Zixin Deng, Lianrong Wang, Shi Chen
Engineering and modifying synthetic microbial chassis is one of the best ways not only to unravel the fundamental principles of life but also to enhance applications in the health, medicine, agricultural, veterinary, and food industries. The two primary strategies for constructing a microbial chassis are the top-down approach (genome reduction) and the bottom-up approach (genome synthesis). Research programs on this topic have been funded in several countries. The 'Minimum genome factory' (MGF) project was launched in 2001 in Japan with the goal of constructing microorganisms with smaller genomes for industrial use...
March 2019: Synthetic and Systems Biotechnology
Yan Li, Lingxin Kong, Jufang Shen, Qing Wang, Qian Liu, Weinan Yang, Zixin Deng, Delin You
Piericidin A1, a member of ɑ-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...
March 2019: Synthetic and Systems Biotechnology
Lei Wang, Meijuan Yuan, Jianting Zheng
The highly reducing iterative polyketide synthases responsible for lovastatin biosynthesis contains a section homologous to condensation (CON) domain observed in nonribosomal peptide synthetases (NRPSs). In the present study, we expressed the isolated lovastatin CON domain and solved the crystal structure to 1.79 Å resolution. The overall structure shows similarity to canonical condensation domains of NRPSs, containing the N-terminal and C-terminal subdomains that resemble enzymes of chloramphenicol acetyltransferase family, whereas distinct structural features are observed at the active site...
March 2019: Synthetic and Systems Biotechnology
Chensi Miao, Huiwei Zhao, Long Qian, Chunbo Lou
With a unique crRNA processing capability, the CRISPR associated Cpf1 protein holds great potential for multiplex gene regulation. Unlike the well-studied Cas9 protein, however, conversion of Cpf1 to a transcription regulator and its related properties have not been systematically explored yet. In this study, we investigated the mutation schemes and crRNA requirements for the DNase deactivated Cpf1 (dCpf1). By shortening the direct repeat sequence, we obtained genetically stable crRNA co-transcripts and improved gene repression with multiplex targeting...
March 2019: Synthetic and Systems Biotechnology
Lian-Hua Xu, Yi-Ling Du
The cytochrome P450 enzymes are ubiquitous heme-thiolate proteins performing regioselective and stereoselective oxygenation reactions in cellular metabolism. Due to their broad substrate scope and catalytic versatility, P450 enzymes are also attractive candidates for many industrial and biopharmaceutical applications. For particular uses, enzyme properties of P450s can be further optimized through directed evolution, rational, and semi-rational engineering approaches, all of which introduce mutations within the P450 structures...
December 2018: Synthetic and Systems Biotechnology
Keqiang Fan, Qian Zhang
Angucyclines are one of the largest families of aromatic polyketides with various chemical structures and bioactivities. Decades of studies have made it easy for us to depict the picture of their early biosynthetic pathways. Two families of oxygenases, the FAD-dependent oxygenases and the ring opening oxygenases, contribute to the formation of some unique skeletons of atypical angucyclines. The FAD-dependent oxygenases involved in the biosynthetic gene clusters of typical angucyclines catalyze two hydroxylation reactions at C-12 and C-12b of prejadomycin, while their homolog JadH in jadomycin gene cluster catalyze the C-12 hydroxylation and 4a,12b-dehydration reactions of prejadomycin, which leads to the production of dehydrorabelomycin, a common intermediate during the biosynthesis of atypical angucyclines...
December 2018: Synthetic and Systems Biotechnology
Xiangyang Liu, Feng Xie, Leah B Doughty, Qi Wang, Lixin Zhang, Xueting Liu, Yi-Qiang Cheng
FK228 is an FDA-approved anticancer drug naturally produced by Chromobacterium violaceum No. 968 up to 19 mg/L in a pilot industry-scale batch fermentation. Here we report a genomics-guided discovery of Burkholderia thailandensis MSMB43 as a new and significantly better source of FK228. The genome of B. thailandensis MSMB43 was found to contain a functional biosynthetic gene cluster highly homologous to that of FK228 in C. violaceum No. 968, and the bacterium indeed produces authentic FK228. By simple fermentation in shaking flasks in a preferred M8 medium, B...
December 2018: Synthetic and Systems Biotechnology
Xihong He, Hong Li, Yuanyuan Pan, Linqi Wang, Huarong Tan, Gang Liu
Streptomyces are the soil-dwelling bacteria with a complex lifecycle and a considerable ability to produce a variety of secondary metabolites. Osmoregulation is important for their lifecycle in nature. In the genome of Streptomyces coelicolor M145, SCO3128 (encodes a putative fatty acid desaturase), SCO3129 (encodes a putative TetR family regulator) and SCO3130 (encodes a putative l-carnitine dehydratase) constitute a transcriptional unit, and its transcript was found to be in response to osmotic stress. Disruption of SCO3130 led to a bald phenotype on MMG medium and the mycelia lysis on the edge of the colony when KCl/NaCl was added to the medium...
December 2018: Synthetic and Systems Biotechnology
Pengwei Li, Zhengyan Guo, Wei Tang, Yihua Chen
Along with the fast developing of DNA sequencing technology, a great number of natural product biosynthetic gene clusters have been discovered by bioinformatic analysis, which demands novel high-throughput genome mining methods to obtain the diverse compounds dictated by those gene clusters. In this work, a method based on the reporter gene xylE was established to screen for the activation conditions of thirteen different gene clusters from Streptomyces lavendulae CGMCC 4.1386. In this reporter-guided method, the key structure gene was replaced by a xylE - kana R cassette with the xylE gene being controlled by the transcription and translation machinery of the key structure gene...
December 2018: Synthetic and Systems Biotechnology
Jin Hou
No abstract text is available yet for this article.
December 2018: Synthetic and Systems Biotechnology
Dongbo Xu, Keshav K Nepal, Jing Chen, Dedra Harmody, Haining Zhu, Peter J McCarthy, Amy E Wright, Guojun Wang
Marine natural products have become an increasingly important source of new drug leads during recent years. In an attempt to identify novel anti-microbial natural products by bioprospecting deep-sea Actinobacteria, three new angucyclines, nocardiopsistins A-C, were isolated from Nocardiopsis sp. strain HB-J378. Notably, the supplementation of the rare earth salt Lanthanum chloride (LaCl3 ) during fermentation of HB-J378 significantly increased the yield of these angucyclines. The structures of nocardiopsistins A-C were identified by 1D and 2D NMR and HR-MS data...
December 2018: Synthetic and Systems Biotechnology
Fei Huang
Lysine acetyltransferases (KATs) catalyze lysine acetylation, a reversible protein modification implicated in a wide variety of disease states. Histone acetyltransferases (HATs) comprise a KAT sub-class that acetylate specific lysines in histones, hence playing an important role in the regulation of chromatin organization and function. HATs are critical regulators of signaling in many diseases, including cancer. KAT6A (also known as monocytic leukemia zinc finger protein, MOZ) and KAT6B (also known as MORF and QKF) belong to the MYST family of HATs, that comprise KAT5-KAT8...
December 2018: Synthetic and Systems Biotechnology
Jiang Zhu, Dongbo Cai, Haixia Xu, Ziwei Liu, Bowen Zhang, Fei Wu, Junhui Li, Shouwen Chen
Bacitracin, a new type of cyclic peptide antibiotic, is widely used as the feed additive in feed industry. Branched chain amino acids (BCAAs) are the key precursors for bacitracin synthesis. In this research, soybean meal was served as the raw material to supply precursor amino acids for bacitracin synthesis, and enhanced production of bacitracin was attempted by engineering BCAA transporter BrnQ and its regulator Lrp in the bacitracin industrial production strain Bacillus licheniformis DW2. Firstly, our results confirmed that Lrp negatively affected bacitracin synthesis in DW2, and deletion of lrp improved intracellular BCAA accumulations, as well as the expression level of BCAA transporter BrnQ, which further led to a 14...
December 2018: Synthetic and Systems Biotechnology
Junhong Wei, Lang He, Guoqing Niu
Actinomycetes are the main sources of antibiotics. The onset and level of production of each antibiotic is subject to complex control by multi-level regulators. These regulators exert their functions at hierarchical levels. At the lower level, cluster-situated regulators (CSRs) directly control the transcription of neighboring genes within the gene cluster. Higher-level pleiotropic and global regulators exert their functions mainly through modulating the transcription of CSRs. Advances in understanding of the regulation of antibiotic biosynthesis in actinomycetes have inspired us to engineer these regulators for strain improvement and antibiotic discovery...
December 2018: Synthetic and Systems Biotechnology
Huayi Liu, Lian Wang, Yunzi Luo
Since 2013, the CRISPR-based bacterial antiviral defense systems have revolutionized the genome editing field. In addition to genome editing, CRISPR has been developed as a variety of tools for gene expression regulations, live cell chromatin imaging, base editing, epigenome editing, and nucleic acid detection. Moreover, in the context of further boosting the usability and feasibility of CRISPR systems, novel CRISPR systems and engineered CRISPR protein mutants have been explored and studied actively. With the flourish of CRISPR technologies, they have been applied in disease treatment recently, as in gene therapy, cell therapy, immunotherapy, and antimicrobial therapy...
December 2018: Synthetic and Systems Biotechnology
Yang Liu, Dayong Yang
Homeostasis widely exists in living systems, and plays essential roles for maintaining normal physiological activities, enabling to preserve their functionalities against variations. Gene expression is a crucial process that allows cells to produce the necessary protein, giving cells the flexibility to adapt to variations. Herein we study homeostasis of gene expression in cell-free system. Heat-inactivated cell lysates and egg white are utilized to create homeostatic microenvironment. Results show that both in cell lysates and egg white, gene expression is maintained at relatively stable levels upon variations including gene amount, magnesium ions and temperature...
December 2018: Synthetic and Systems Biotechnology
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