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Recent Synthetic and Systems Biotechnology Articles

Recently published articles from Synthetic and Systems Biotechnology.

Streamlining the preparation of “endotoxin-free” ClearColi cell extract with autoinduction media for cell-free protein synthesis of the therapeutic protein crisantaspase

An “endotoxin-free” E. coli-based cell-free protein synthesis system has been reported to produce therapeutic proteins rapidly and on-demand. However, preparation of the most complex CFPS reagent –...

Resolution of deep divergence of club fungi (phylum Basidiomycota)

December 2019
Hongliang Mao | Hao Wang

A long-standing question about the early evolution of club fungi (phylum Basidiomycota) is the relationship between the three major groups, Pucciniomycotina, Ustilaginomycotina and Agaricomycotina....

Phosphate limitation increases coenzyme Q10 production in industrial Rhodobacter sphaeroides HY01

Coenzyme Q10 (CoQ10) is an important component of the respiratory chain in humans and some bacteria. As a high-value-added nutraceutical antioxidant, CoQ10 has excellent capacity to prevent cardiovascular...

Methods to reduce variability in E. Coli-based cell-free protein expression experiments

December 2019
Jared L. Dopp | Yeong Ran Jo | Nigel F. Reuel

Cell-free protein synthesis (CFPS) is an established biotechnology tool that has shown great utility in many applications such as prototyping proteins, building genetic circuits, designing biosensors,...

Engineering strong and stress-responsive promoters in Bacillus subtilis by interlocking sigma factor binding motifs

Prokaryotic gene expression is largely regulated on transcriptional levels with the involvement of promoters, RNA polymerase and sigma factors. Developing new promoters to customize gene transcriptional...

Simplified methodology for a modular and genetically expanded protein synthesis in cell-free systems

Genetic code expansion, which enables the site-specific incorporation of unnatural amino acids into proteins, has emerged as a new and powerful tool for protein engineering. Currently, it is mainly...

Benchmarking two Saccharomyces cerevisiae laboratory strains for growth and transcriptional response to methanol

December 2019
Monica I. Espinosa | Thomas C. Williams | Isak S. Pretorius | Ian T. Paulsen

One-carbon compounds, such as methanol, are becoming potential alternatives to sugars as feedstocks for the biological production of chemicals, fuels, foods, and pharmaceuticals. Efficient biological...

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

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

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

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...

The road less traveled: A new phosphorothioate antiviral defense mechanism discovered in Archaea

September 2019
Michael S. DeMott | Peter C. Dedon

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

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

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

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

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

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

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

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

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

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

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

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...

Creating an oil yeast from brewing yeast

December 2018
Jin Hou

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

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...

CRISPR-Cas9/Cas12a biotechnology and application in bacteria

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...

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

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...

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