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Recent Synthetic and Systems Biotechnology Articles

Recently published articles from Synthetic and Systems Biotechnology.

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...

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...

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,...

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,...

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...

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...

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...

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,...

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...

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....

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 –...

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...

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...

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...

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...

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...

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