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Recent Synthetic and Systems Biotechnology Articles

Recently published articles from Synthetic and Systems Biotechnology.

Brocaeloid D, a novel compound isolated from a wheat pathogenic fungus, Microdochium majus 99049

December 2019
Jingyu Zhang | Zhenzhen Wang | Zhijun Song | Loganathan Karthik | Chengjian Hou | Guoliang Zhu | Lan Jiang | Jianying Han | Rong Ma | Li Li | Lixin Zhang | Xueting Liu | Tom Hsiang

Microbes serve as the most important resource for drug discovery. During our screening for bioactive compounds from our natural products library, a pathogenic fungus, Microdochium majus strain 99049,...

Detailed profiling of carbon fixation of in silico synthetic autotrophy with reductive tricarboxylic acid cycle and Calvin-Benson-Bassham cycle in Esherichia coli using hydrogen as an energy source

September 2019
Hsieh-Ting-Yang Cheng | Shou-Chen Lo | Chieh-Chen Huang | Tsung-Yi Ho | Ya-Tang Yang

Carbon fixation is the main route of inorganic carbon in the form of CO2 into the biosphere. In nature, RuBisCO is the most abundant protein that photosynthetic organisms use to fix CO2 from the atmosphere...

A novel D(−)-lactic acid-inducible promoter regulated by the GntR-family protein D-LldR of Pseudomonas fluorescens

September 2019
Kalpana Singh | Satish Kumar Ainala | Yeonhee Kim | Sunghoon Park

Lactic acid has two stereoisomers of D(−)- and L(+)-forms, both of which are important monomers of biodegradable plastic, poly-lactic acid. In this study, a novel d-lactate inducible system was identified...

The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer

September 2019
Guan-Da Huang | Xue-Mei Liu | Tian-Lai Huang | Li- C. Xia

Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer (HGT). However, with the rapid increase of sequencing depth, hundreds of thousands of contigs...

Depiction of secondary metabolites and antifungal activity of Bacillus velezensis DTU001

September 2019
Sagarika Devi | Heiko T. Kiesewalter | Renátó Kovács | Jens Christian Frisvad | Tilmann Weber | Thomas Ostenfeld Larsen | Ákos T. Kovács | Ling Ding

For a safe and sustainable environment, effective microbes as biocontrol agents are in high demand. We have isolated a new Bacillus velezensis strain DTU001, investigated its antifungal spectrum, sequenced...

Efficient biosynthesis of 2-keto-D-gluconic acid by fed-batch culture of metabolically engineered Gluconobacter japonicus

September 2019
Weizhu Zeng | Wen Cai | Li Liu | Guocheng Du | Jian Chen | Jingwen Zhou

2-keto-d-gluconic acid (2-KGA) is a key precursor for synthesising vitamin C and isovitamin C. However, phage contamination is as constant problem in industrial production of 2-KGA using Pseudomonas...

A novel synchronization approach using synthetic magnetic Escherichia coli

September 2019
Hua Ling | Matthew Wook Chang

The group headed by Professor Chenli Liu in the Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT) recently developed a microfluidic synchronizer to continuously produce...

Metabolic engineering of Corynebacterium glutamicum S9114 based on whole-genome sequencing for efficient N-acetylglucosamine synthesis

September 2019
Chen Deng | Xueqin Lv | Yanfeng Liu | Jianghua Li | Wei Lu | Guocheng Du | Long Liu

Glucosamine (GlcN) and its acetylated derivative N-acetylglucosamine (GlcNAc) are widely used in the pharmaceutical industries. Here, we attempted to achieve efficient production of GlcNAc via genomic...

Genomic and transcriptional changes in response to pinene tolerance and overproduction in evolved Escherichia coli

September 2019
Fu-Xing Niu | Yuan-Bin Huang | Liang-Nian Ji | Jian-Zhong Liu

α-Pinene is an important monoterpene, which is widely used as a flavoring agent and in fragrances, pharmaceuticals and biofuels. Although an evolved strain Escherichia coli YZFP, which had higher tolerance...

The phage T4 DNA ligase mediates bacterial chromosome DSBs repair as single component non-homologous end joining

June 2019
Tianyuan Su | Fapeng Liu | Yizhao Chang | Qi Guo | Junshu Wang | Qian Wang | Qingsheng Qi

DNA double-strand breaks (DSBs) are one of the most lethal forms of DNA damage that is not efficiently repaired in prokaryotes. Certain microorganisms can handle chromosomal DSBs using the error-prone...

Design and synthesis of synthetic UP elements for modulation of gene expression in Escherichia coli

June 2019
Kristin V. Presnell | Madeleine Flexer-Harrison | Hal S. Alper

Metabolic engineering requires fine-tuned gene expression for most pathway optimization applications. To develop a suitable suite of promoters, traditional bacterial promoter engineering efforts have...

Resistance mechanisms and reprogramming of microorganisms for efficient biorefinery under multiple environmental stresses

June 2019
Ke Xu | Yun Seo Lee | Jun Li | Chun Li

In the fermentation process of biorefinery, industrial strains are normally subjected to adverse environmental stresses, which leads to their slow growth, yield decline, a substantial increase in energy...

Efficient editing DNA regions with high sequence identity in actinomycetal genomes by a CRISPR-Cas9 system

June 2019
Jingjun Mo | Shuwen Wang | Wan Zhang | Chunyu Li | Zixin Deng | Lixin Zhang | Xudong Qu

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...

Simultaneously down-regulation of multiplex branch pathways using CRISPRi and fermentation optimization for enhancing β-amyrin production in Saccharomyces cerevisiae

June 2019
Jiangping Ni | Genlin Zhang | Lei Qin | Jun Li | Chun Li

The production of β-amyrin in Saccharomyces cerevisiae is still low due to the inability of effectively regulating the endogenous metabolic pathway for competitive synthesis of β-amyrin precursors....

CRISPR-PIN: Modifying gene position in the nucleus via dCas9-mediated tethering

June 2019
Jyun-Liang Lin | Holly Ekas | Matthew Deaner | Hal S. Alper

Spatial organization of DNA within the nucleus is important for controlling DNA replication and repair, genetic recombination, and gene expression. Here, we present CRISPR-PIN, a CRISPR/dCas9-based...

Synergistic drug combinations prediction by integrating pharmacological data

March 2019
Chengzhi Zhang | Guiying Yan

There is compelling evidence that synergistic drug combinations have become promising strategies for combating complex diseases, and they have evident predominance comparing to traditional one drug...

Miniaturisation of high-throughput plasmid DNA library preparation for next-generation sequencing using multifactorial optimisation

March 2019
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...

Comparative functional genomics of the acarbose producers reveals potential targets for metabolic engineering

March 2019
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 LuxR family transcriptional regulator AniF promotes the production of anisomycin and its derivatives in Streptomyces hygrospinosus var. beijingensis

March 2019
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...

Streptomyces avermitilis industrial strain as cell factory for Ivermectin B1a production

March 2019
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 C22C23 position. Combinatorial biosynthesis of Ivermectins based on Avermectins biosynthetic...

Characterization of the positive SARP family regulator PieR for improving piericidin A1 production in Streptomyces piomogeues var. Hangzhouwanensis

March 2019
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...

Engineering and modification of microbial chassis for systems and synthetic biology

March 2019
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,...

Crystal structure of the condensation domain from lovastatin polyketide synthase

March 2019
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)....

Systematically investigating the key features of the DNase deactivated Cpf1 for tunable transcription regulation in prokaryotic cells

March 2019
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...

Thank you note

December 2018

The functional differentiation of the post-PKS tailoring oxygenases contributed to the chemical diversities of atypical angucyclines

December 2018
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...

Genomics-guided discovery of a new and significantly better source of anticancer natural drug FK228

December 2018
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...

Enhancement of precursor amino acid supplies for improving bacitracin production by activation of branched chain amino acid transporter BrnQ and deletion of its regulator gene lrp in Bacillus licheniformis

December 2018
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...

New KAT6 inhibitors induce senescence and arrest cancer growth

December 2018
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...

Nocardiopsistins A-C: New angucyclines with anti-MRSA activity isolated from a marine sponge-derived Nocardiopsis sp. HB-J378

December 2018
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...

Activation of three natural product biosynthetic gene clusters from Streptomyces lavendulae CGMCC 4.1386 by a reporter-guided strategy

December 2018
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...

SCO3129, a TetR family regulator, is responsible for osmotic stress in Streptomyces coelicolor

December 2018
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....

Regulation of antibiotic biosynthesis in actinomycetes: Perspectives and challenges

December 2018
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...

Cell lysates and egg white create homeostatic microenvironment for gene expression in cell-free system

December 2018
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...

Blossom of CRISPR technologies and applications in disease treatment

December 2018
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...

Rational and semi-rational engineering of cytochrome P450s for biotechnological applications

December 2018
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...

Therapeutic applications of genetic code expansion

September 2018
Yujia Huang | Tao Liu

In nature, a limited, conservative set of amino acids are utilized to synthesize proteins. Genetic code expansion technique reassigns codons and incorporates noncanonical amino acids (ncAAs) through...

CRISPR-Cas9/Cas12a biotechnology and application in bacteria

September 2018
Ruilian Yao | Di Liu | Xiao Jia | Yuan Zheng | Wei Liu | Yi Xiao

CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and...

Substrate specificity of the cypemycin decarboxylase CypD

September 2018
Wei Ding | Tianlu Mo | Dhanaraju Mandalapu | Qi Zhang

The linaridin antibiotic cypemycin is a ribosomal synthesized and post-translationally modified peptide (RiPP) that possesses potent activity against mouse leukemia cells. This peptide natural product...

Activation of microbial secondary metabolic pathways: Avenues and challenges

September 2018
Bikash Baral | Amir Akhgari | Mikko Metsä-Ketelä

Microbial natural products are a tremendous source of new bioactive chemical entities for drug discovery. Next generation sequencing has revealed an unprecedented genomic potential for production of...

Synthetic immunology: T-cell engineering and adoptive immunotherapy

September 2018
Wen Si | Cheng Li | Ping Wei

During the past decades, the rapidly-evolving cancer is hard to be thoroughly eliminated even though the radiotherapy and chemotherapy do exhibit efficacy in some degree. However, a breakthrough appeared...

Conversion of d-glucose to l-lactate via pyruvate by an optimized cell-free enzymatic biosystem containing minimized reactions

September 2018
Leipeng Xie | Xinlei Wei | Xigui Zhou | Dongdong Meng | Ruimin Zhou | Yi-Heng P. Job Zhang | Shuxia Xu | Chun You

Cell-free synthetic enzymatic biosystem is emerging to expand the traditional biotechnological mode by utilizing a number of purified/partially purified enzymes and coenzymes in a single reaction vessel...

A genetically engineered Escherichia coli that senses and degrades tetracycline antibiotic residue

September 2018
Zepeng Mu | Zhuoning Zou | Ye Yang | Wenbo Wang | Yue Xu | Jianyi Huang | Ruiling Cai | Ye Liu | Yajin Mo | Boyi Wang | Yiqun Dang | Yongming Li | Yushan Liu | Yueren Jiang | Qingyang Tan | Xiaohong Liu | Cheng Hu | Hua Li | Sha Wei | Chunbo Lou | Yang Yu | Jiangyun Wang

Due to the abuse of antibiotics, antibiotic residues can be detected in both natural environment and various industrial products, posing threat to the environment and human health. Here we describe...

An in vitro synthetic biology platform for emerging industrial biomanufacturing: Bottom-up pathway design

September 2018
Ting Shi | Pingping Han | Chun You | Yi-Heng P. Job Zhang

Although most in vitro (cell-free) synthetic biology projects are usually used for the purposes of fundamental research or the formation of high-value products, in vitro synthetic biology platform,...

RiPPing apart the rules for peptide natural products

June 2018
Aman S. Imani | Michael F. Freeman

Synergistic and non-specific nucleic acid production by T7 RNA polymerase and Bsu DNA polymerase catalyzed by single-stranded polynucleotides

June 2018
Nicholas J. Emery | Sagardip Majumder | Allen P. Liu

Point-of-care molecular diagnostic tests show great promise for providing accurate, timely results in low-infrastructure healthcare settings and at home. The design space for these tests is limited...

Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology

June 2018
Lihong Jiang | Jiarun Zhao | Jiazhang Lian | Zhinan Xu

Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade....

Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics

June 2018
Ryohei Narumi | Keiko Masuda | Takeshi Tomonaga | Jun Adachi | Hiroki R. Ueda | Yoshihiro Shimizu

High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation...

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