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Recent Synthetic and Systems Biotechnology Articles

Recently published articles from Synthetic and Systems Biotechnology.

Complex natural product production methods and options

March 2021
Dongwon Park | Girish Swayambhu | Thomas Lyga | Blaine A. Pfeifer

Natural products have had a major impact upon quality of life, with antibiotics as a classic example of having a transformative impact upon human health. In this contribution, we will highlight both...

Advances on systems metabolic engineering of Bacillus subtilis as a chassis cell

December 2020
Mengjie Xiang | Qian Kang | Dawei Zhang

The Gram-positive model bacterium Bacillus subtilis, has been broadly applied in various fields because of its low pathogenicity and strong protein secretion ability, as well as its well-developed fermentation...

Methodologies for preparation of prokaryotic extracts for cell-free expression systems

December 2020
Stephanie D. Cole | Aleksandr E. Miklos | Abel C. Chiao | Zachary Z. Sun | Matthew W. Lux

Cell-free systems that mimic essential cell functions, such as gene expression, have dramatically expanded in recent years, both in terms of applications and widespread adoption. Here we provide a review...

Expanding application of CRISPR-Cas9 system in microorganisms

December 2020
Jing Zhao | Huan Fang | Dawei Zhang

The development of CRISPR-Cas9 based genetic manipulation tools represents a huge breakthrough in life sciences and has been stimulating research on metabolic engineering, synthetic biology, and systems...

CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants

December 2020
Abdullah | Zhengzheng Jiang | Xulin Hong | Shun Zhang | Ruilian Yao | Yi Xiao

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated) has been extensively exploited as a genetic tool for genome editing. The RNA guided Cas nucleases generate DNA...

Emerging biosensors in detection of natural products

December 2020
Firoozeh Piroozmand | Fatemeh Mohammadipanah | Farnoush Faridbod

Natural products (NPs) are a valuable source in the food, pharmaceutical, agricultural, environmental, and many other industrial sectors. Their beneficial properties along with their potential toxicities...

Microbial electro-fermentation for synthesis of chemicals and biofuels driven by bi-directional extracellular electron transfer

December 2020
Ziying Gong | Huan Yu | Junqi Zhang | Feng Li | Hao Song

Electroactive bacteria could perform bi-directional extracellular electron transfer (EET) to exchange electrons and energy with extracellular environments, thus playing a central role in microbial electro-fermentation...

Enhancing single-cell hyaluronic acid biosynthesis by microbial morphology engineering

December 2020
Yukun Zheng | Fangyu Cheng | Bo Zheng | Huimin Yu

Microbial morphology engineering is a novel approach for cell factory to improve the titer of target product in bio-manufacture. Hyaluronic acid (HA), a valuable glycosaminoglycan polymerized by HA...

Converting Escherichia coli MG1655 into a chemical overproducer through inactivating defense system against exogenous DNA

December 2020
Jingge Wang | Chaoyong Huang | Kai Guo | Lianjie Ma | Xiangyu Meng | Ning Wang | Yi-Xin Huo

Escherichia coli strain K-12 MG1655 has been proposed as an appropriate host strain for industrial production. However, the direct application of this strain suffers from the transformation inefficiency...

Applications of phage-derived RNA-based technologies in synthetic biology

December 2020
Wenhui Zhang | Qiong Wu

As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering...

Physical stimuli-responsive cell-free protein synthesis

December 2020
Junzhu Yang | Yuan Lu

Cell-free protein synthesis has been developed as a critical platform in synthetic biology. Unlike the cell-based synthesis system, cell-free system activates transcriptional and translational mechanisms...

Cell-free synthesis system-assisted pathway bottleneck diagnosis and engineering in Bacillus subtilis

September 2020
Rongzhen Tian | Minghu Wang | Jintian Shi | Xiaolong Qin | Haoyu Guo | Xuanjie Jia | Jianghua Li | Long Liu | Guocheng Du | Jian Chen | Yanfeng Liu

Metabolic engineering is a key technology for cell factories construction by rewiring cellular resources to achieve efficient production of target chemicals. However, the existence of bottlenecks in...

Improving the reaction mix of a Pichia pastoris cell-free system using a design of experiments approach to minimise experimental effort

September 2020
Alex J. Spice | Rochelle Aw | Daniel G. Bracewell | Karen M. Polizzi

A renaissance in cell-free protein synthesis (CFPS) is underway, enabled by the acceleration and adoption of synthetic biology methods. CFPS has emerged as a powerful platform technology for synthetic...

Metabolic engineering of a methyltransferase for production of drug precursors demecycline and demeclocycline in Streptomyces aureofaciens

September 2020
Weinan Yang | Lingxin Kong | Qing Wang | Zixin Deng | Delin You

Demecycline (DMTC) and demeclocycline (DMCTC) are C6-demethylated derivatives of tetracycline (TC) and chlortetracycline (CTC), respectively. They are precursors of minocycline and tigecycline, which...

Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs)

September 2020
Zheng Zhong | Beibei He | Jie Li | Yong-Xin Li

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of cyclic or linear peptidic natural products with remarkable structural and functional diversity. Recent advances...

Silk fibroin as an additive for cell-free protein synthesis

September 2020
Marilyn S. Lee | Chia-Suei Hung | Daniel A. Phillips | Chelsea C. Buck | Maneesh K. Gupta | Matthew W. Lux

Cell-free systems contain many proteins and metabolites required for complex functions such as transcription and translation or multi-step metabolic conversions. Research into expanding the delivery...

From nature to nurture: Essence and methods to isolate robust methanotrophic bacteria

September 2020
Haritha Meruvu | Hui Wu | Ziyue Jiao | Liyan Wang | Qiang Fei

Methanotrophic bacteria are entities with innate biocatalytic potential to biofilter and oxidize methane into simpler compounds concomitantly conserving energy, which can contribute to copious industrial...

Discovery and modification of cytochrome P450 for plant natural products biosynthesis

September 2020
Xiaonan Liu | Xiaoxi Zhu | Hui Wang | Tian Liu | Jian Cheng | Huifeng Jiang

Cytochrome P450s are widespread in nature and play key roles in the diversification and functional modification of plant natural products. Over the last few years, there has been remarkable progress...

Harnessing sub-organelle metabolism for biosynthesis of isoprenoids in yeast

September 2020
Xuan Cao | Shan Yang | Chunyang Cao | Yongjin J. Zhou

Current yeast metabolic engineering in isoprenoids production mainly focuses on rewiring of cytosolic metabolic pathway. However, the precursors, cofactors and the enzymes are distributed in various...

Engineering Escherichia coli to improve tryptophan production via genetic manipulation of precursor and cofactor pathways

September 2020
Zhu Li | Dongqin Ding | Huiying Wang | Linxia Liu | Huan Fang | Tao Chen | Dawei Zhang

Optimizing the supply of biosynthetic precursors and cofactors is usually an effective metabolic strategy to improve the production of target compounds. Here, the combination of optimizing precursor...

Positional assembly of multi-enzyme cascade reaction in polyelectrolyte doped microcapsule through electrospray and layer-by-layer assembly

September 2020
Shiyi Che | Jie Wang | Xiaoyuan Ji | Zhiguo Su | Shaomin Wang | Songping Zhang

Polyelectrolyte-doped microcapsules (PDM) was fabricated by coaxial electrospray of a mixture of glycerol and water containing 10 mg/mL cationic polyelectrolyte poly(allylamine hydrochloride) (PAH)...

Mining and fine-tuning sugar uptake system for titer improvement of milbemycins in Streptomyces bingchenggensis

September 2020
Pinjiao Jin | Shanshan Li | Yanyan Zhang | Liyang Chu | Hairong He | Zhuoxu Dong | Wensheng Xiang

Dramatic decrease of sugar uptake is a general phenomenon in Streptomyces at stationary phase, when antibiotics are extensively produced. Milbemycins produced by Streptomyces bingchenggensis are a group...

Unstructured kinetic models to simulate an arabinose switch that decouples cell growth from metabolite production

September 2020
Harley Edwards | Peng Xu

Modeling synthetic gene circuits to implement dynamic flux balancing is crucial in teaching and exploring metabolic engineering strategies to repartition metabolic precursors and construct efficient...

Redesigning transcription factor Cre1 for alleviating carbon catabolite repression in Trichoderma reesei

September 2020
Lijuan Han | Kuimei Liu | Wei Ma | Yi Jiang | Shaoli Hou | Yinshuang Tan | Quanquan Yuan | Kangle Niu | Xu Fang

Carbon catabolite repression (CCR), which is mainly mediated by Cre1 and triggered by glucose, leads to a decrease in cellulase production in Trichoderma reesei. Many studies have focused on modifying...

Structure-guided manipulation of the regioselectivity of the cyclosporine A hydroxylase CYP-sb21 from Sebekia benihana

September 2020
Fengwei Li | Li Ma | Xingwang Zhang | Jingfei Chen | Feifei Qi | Yinyue Huang | Zepeng Qu | Lishan Yao | Wei Zhang | Eung-Soo Kim | Shengying Li

The cytochrome P450 enzyme CYP-sb21 from the rare actinomycete Sebekia benihana is capable of hydroxylating the immunosuppressive drug molecule cyclosporine A (CsA) primarily at the 4th N-methyl leucine...

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

June 2020
Peng Gao | Shiwen Ma | Daru Lu | Carl Mitcham | Yijia Jing | Guoyu Wang

In response to the outbreak of COVID-19 that has been sweeping the world, scientists reconstructed the SARS-CoV-2 rapidly using a synthetic genomics platform, in order to accelerate therapeutics and...

Complete genome sequence of high-yield strain S. lincolnensis B48 and identification of crucial mutations contributing to lincomycin overproduction

June 2020
Ruida Wang | Fanjing Kong | Haizhen Wu | Bingbing Hou | Yajing Kang | Yuan Cao | Shiwei Duan | Jiang Ye | Huizhan Zhang

The lincosamide family antibiotic lincomycin is a widely used antibacterial pharmaceutical generated by Streptomyces lincolnensis, and the high-yield strain B48 produces 2.5 g/L lincomycin, approximately...

Coordinated regulation for nature products discovery and overproduction in Streptomyces

June 2020
Qun Zhou | Shuqing Ning | Yunzi Luo

Streptomyces is an important treasure trove for natural products discovery. In recent years, many scientists focused on the genetic modification and metabolic regulation of Streptomyces to obtain diverse...

Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases

June 2020
Erin E. Drufva | Elijah G. Hix | Constance B. Bailey

Modular polyketide synthases (PKSs) are a multidomain megasynthase class of biosynthetic enzymes that have great promise for the development of new compounds, from new pharmaceuticals to high value...

Toward fine-tuned metabolic networks in industrial microorganisms

June 2020
Ning Li | Weizhu Zeng | Sha Xu | Jingwen Zhou

There are numerous microorganisms in nature capable of synthesizing diverse useful compounds; however, these natural microorganisms are generally inefficient in the production of target products on...

An aurora of natural products-based drug discovery is coming

June 2020
Yaojun Tong | Zixin Deng

Natural products (NPs), a nature's reservoir possessing enormous structural and functional diversity far beyond the current ability of chemical synthesis, are now proving themselves as most wonderful...

Designing sgRNAs for CRISPR-BEST base editing applications with CRISPy-web 2.0

June 2020
Kai Blin | Simon Shaw | Yaojun Tong | Tilmann Weber

CRISPR/Cas9 systems are an established tool in genome engineering. As double strand breaks caused by the standard Cas9-based knock-out techniques can be problematic in some organisms, new systems were...

A high stable pH-temperature dual-sensitive liposome for tuning anticancer drug release

June 2020
Yilin Zhao | Fuli Cai | Xiangyi Shen | Haijia Su

In order to improve the targeting and availability of liposomes to cancer cells, the temperature sensitivity of 1, 2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and the pH sensitivity of PASP in...

Application of serine integrases for secondary metabolite pathway assembly in Streptomyces

June 2020
Hong Gao | Gabrielle Taylor | Stephanie K. Evans | Paul C.M. Fogg | Margaret C.M. Smith

Serine integrases have been shown to be efficient tools for metabolic pathway assembly. To further improve the flexibility and efficiency of pathway engineering via serine integrases, we explored how...

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...

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...

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