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Recent Synthetic and Systems Biotechnology Articles

Recently published articles from Synthetic and Systems Biotechnology.

Prudently conduct the engineering and synthesis of the SARS-CoV-2 virus

Available online 2 April 2020
Shiwen Ma | Peng Gao | Daru Lu | Guoyu Wang

Regarding to the recent work of engineering SARS-CoV-19 virus and the publication “Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform” by researchers at University of Bern, this...

Designing chimeric enzymes inspired by fungal cellulosomes

March 2020
Sean P. Gilmore | Stephen P. Lillington | Charles H. Haitjema | Randall de Groot | Michelle A. O'Malley

Cellulosomes are synthesized by anaerobic bacteria and fungi to degrade lignocellulose via synergistic action of multiple enzymes fused to a protein scaffold. Through templating key protein domains...

Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast

March 2020
Tadas Jakočiūnas | Andreas K. Klitgaard | Eftychia Eva Kontou | Julie Bang Nielsen | Emil Thomsen | David Romero-Suarez | Kai Blin | Christopher J. Petzold | Jennifer W. Gin | Yaojun Tong | Charlotte Held Gotfredsen | Pep Charusanti | Rasmus J.N. Frandsen | Tilmann Weber | Sang Yup Lee | Michael K. Jensen | Jay D. Keasling

To accelerate the shift to bio-based production and overcome complicated functional implementation of natural and artificial biosynthetic pathways to industry relevant organisms, development of new,...

Unlocking a new target for streptomycetes strain improvement

March 2020
Yuan Chen | Jackie Metz | René K. Miller-Xavier | Guojun Wang

Biofilm architecture: An emerging synthetic biology target

March 2020
Stephen J. Kassinger | Monique L. van Hoek

Synthetic biologists are exploiting biofilms as an effective mechanism for producing various outputs. Metabolic optimization has become commonplace as a method of maximizing system output. In addition...

Unleashing the power of energy storage: Engineering β-oxidation pathways for polyketide production

March 2020
Bin Wang | Huimin Zhao

Overproduction of polyketides has been a challenge for metabolic engineering for decades. However, recent studies have demonstrated that in both native host and heterologous host, engineering β -oxidation...

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

December 2019
J. Porter Hunt | Emily Long Zhao | Mehran Soltani | Madison Frei | J. Andrew D. Nelson | Bradley C. Bundy

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

December 2019
Lu Zhang | Leshi Liu | Ke-Feng Wang | Lan Xu | Liming Zhou | Weishan Wang | Chuan Li | Zheng Xu | Tong Shi | Haihong Chen | Yuanhang Li | Hui Xu | XiuLiang Yang | Zhichun Zhu | Biqin Chen | Dan Li | Guanghuang Zhan | Si-Liang Zhang | Li-Xin Zhang | Gao-Yi Tan

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

December 2019
Yang Wang | Yanan Shi | Litao Hu | Guocheng Du | Jian Chen | Zhen Kang

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

December 2019
Yonatan Chemla | Eden Ozer | Michael Shaferman | Ben Zaad | Rambabu Dandela | Lital Alfonta

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

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...

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...

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....

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...

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