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Table of Content

    31 December 2020, Volume 1 Issue 6
    Contents
    2020, 1(6):  0. 
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    Invited Review
    Research advances in synthetic microbial communities
    Zepeng QU, Moxian CHEN, Zhaohui CAO, Wenlong ZUO, Ye CHEN, Lei DAI
    2020, 1(6):  621-634.  doi:10.12211/2096-8280.2020-012
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    Synthetic microbial communities are an emerging research field at the intersection of synthetic biology and microbiome. A synthetic microbial community is created artificially by co-culturing of multiple species under a well-defined condition. Synthetic communities that retain the key features of their natural counterparts can act as a model system to study the ecology and function of microbial communities in a controlled way. This review covers important topics and research progress in synthetic microbial communities. We start with a summary of ecological factors that shape the structure of microbial communities, including interactions among microbes, host metabolism and immunity and environmental conditions. We then discuss the methods and experimental techniques in design-build-test-learn (DBTL) cycle, used to study synthetic microbial communities. In addition, we review the potential applications of synthetic microbiome in human health, agriculture, industrial production and environmental remediation. Finally, we summarize key scientific questions for future studies of synthetic microbial communities,including how to construct a controllable and stable microbial interaction network, how to characterize and manage the spatial structure of microbial communities, and how to accurately shape the function of microbial communities.

    Advances and applications of phage synthetic biology
    Shengjian YUAN, Yingfei MA
    2020, 1(6):  635-655.  doi:10.12211/2096-8280.2020-027
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    Bacteriophage (phage) are viruses that specifically infect bacterial and archaea. Phage is the most diverse and abundant biological entity on the planet. For more than a century, phage is one of the most important model organisms in the molecular biological research. Many important discoveries upon phage research have enabled us to understand the mechanisms of genetic materials in biological activities, and many phage-derived enzymes are greatly useful in the molecular biological research. Phage has also been recognized as natural antimicrobial agents for treating the bacterial infections. In particular, nowadays, the concern related to the emergence of bacteria resistance to multiple antibiotics is increasing. However, the challenges in phage therapy, such as narrow host range and bacterial resistance, limited the application of phage therapy in treating the diseases of antibiotic-resistant bacterial infections. Novel strategies are needed to be developed to overcome the hurdles associated with phage therapy. Synthetic biology aims to design and reprogram new biological systems according to the known principles. Because of their relatively small genome size (5—735 kb), fast growth rate, ease of genetic manipulation, and simple structure, phages have become the most important biological system for synthetic biology research. In this review, we discuss the advances of synthetic biology facing the major challenges of natural phages in basic and application research. For example, synthetic biology has been applied to enhance the infection efficiency of phages, improve the phage biosafety, alter the phage host ranges, adjust the bacterial communities, and knock out the specific bacterial genes. We also present some examples to show the methods that were widely used for phage engineering to obtain phages with new functions. In addition, phage display and phage-assisted continuous evolution have also become powerful tools in synthetic biology. In short, the development of synthetic biology will inspire scientists to design modular phages as multifunctional biological agents for clearance of multi-drug resistant bacteria, detection of the pathogen, regulation of bacterial diversity, and drug delivery.

    Progress and prospective of engineering microbial cell factories: from random mutagenesis to customized design in genome scale
    Yaomeng YUAN, Xinhui XING, Chong ZHANG
    2020, 1(6):  656-673.  doi:10.12211/2096-8208.2020-050
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    As the core of green bio-manufacturing and bioeconomy, microbial cell factories (MCFs) are widely used to produce a variety of chemicals, foods, medicines and fuels. In the early years, isolation and random mutagenesis of natural microbes were time-consuming but widely used for developing well-performed MCFs. With the development of molecular biology and genetic engineering, the advancements in understanding of microbial systems prompted the establishment of metabolic engineering. Nowadays, different MCF-construction strategies in terms of protein, pathway and genome-wide engineering have been well developed based on rational or semi-rational metabolic engineering strategies. However, due to limited biological knowledge, these strategies mainly rely on the iterative cycle of ‘Design-Build-Test-Learning (DBTL)’, usually taking 50—300 person-years and hundreds of millions of dollars to develop a MCF that can meet industrial demands. Combining high-throughput genome editing and phenotype screening and selection technologies, the genome-wide customized engineering allows one to obtain large-scale genotype-phenotype association (GPA) data sets quickly. Based on these results, data science technologies can be further applied to mine a large number of unknown genes or loci associated with the specific phenotypes. This strategy has a wider search scope for genotype (genome-wide) and does not rely on existing biological knowledge (data-driven), thus making it possible to explore phenotypes that could not be achieved by the above mentioned rational/semi-rational strategies and develop MCFs with superior performance more efficiently. This paper reviews general strategies and application cases for the design and construction of MCFs. We will firstly summarize the overview of random mutagenesis strategies, and the history and latest progress in metabolic engineering for the construction of MCFs. Then we discuss the potential of the newly emerging MCF-design and construction paradigm, and the customized design strategies at the whole genome scales. Finally, we conclude with our perspectives on the development of novel strategies for the engineering of MCFs.

    Construction and application of microbial cell factories for production of bulk chemicals
    Yong YU, Xinna ZHU, Xueli ZHANG
    2020, 1(6):  674-684.  doi:10.12211/2096-8280.2020-049
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    With the development of synthetic biology, more and more bulk chemicals can be produced through microbial cell factories, which can avoid the dependence on petroleum resources and decrease energy cost and pollution. In this review, the key technologies for construction of microbial cell factories were firstly introduced, including genome editing, simultaneous modulation of multiple genes, protein scaffold, gene dynamic modulation and high throughput screening technologies. How to characterize the metabolic regulation mechanisms for efficient production of chemicals was then introduced in three aspects: carbon metabolism, energy metabolism and physiological metabolism, and succinate cell factory was used as an example. Successful bulk chemical cell factories in recent years were then summarized, including L-alanine, L-methionine, succinate, D-lactate, malonate, L-malate, glutarate, adipate, 1,3-propanediol, 1,4-butanediol, isobutanol, etc. In the future, further increasing the efficiency of substrates utilization and broadening the range of products will be the directions of development of microbial cell factories, but the design and engineering of new enzymes are the key bottleneck limiting the design of metabolic pathways. It is believed that with the deepening of research, microbial cell factories will be more widely used in the production of bulk chemicals besides chemical methods.

    Artificial enzyme designs and its application based on non-natural structural elements
    Feiyan YUAN, Yang YU, Chun LI
    2020, 1(6):  685-696.  doi:10.12211/2096-8280.2020-008
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    Artificial enzymes are catalysts designed by humans beings with similar activities to those of natural enzymes. The design of artificial enzymes may be a supplement for the study of natural enzymes, which can reveal the catalytic mechanism of natural enzymes and lead to catalysts for novel reactions. Enzymes are composed of 20 kinds of natural amino acids residues and a limited number of cofactors, which limits the structure, reactivity and functional space that proteins can access. Artificial enzymes with high catalytic activity or novel reactivity can be obtained by introducing non-natural structural components, including unnatural amino acids and non-natural cofactors into proteins. This article summarizes strategies for construction of artificial enzymes and efficient preparations of such artificial enzymes with unnatural amino acids and non-natural cofactors. Taking artificial metalloenzymes involved in the redox reactions as examples, this review discusses methods to construct artificial enzymes through introduction of unnatural amino acids containing bio-orthogonal reaction groups or metal chelating groups by genetic codon expansion, or through introduction of non-natural metalloporphyrins and other organometallic catalysts into scaffold proteins by covalent or non-covalent attachments. Emerging methods for construction of artificial enzymes using non-natural structural elements combined with computational design or metabolic engineering is prospected. These will be helpful to accelerate the design and preparation of artificial enzymes, leading to artificial enzymes with comparable activities to the native enzymes, and they will have great potential for industrial applications.

    Advances in technologies for de novo DNA synthesis, assembly and error correction
    Kai PENG, Xiaoyun LU, Jian CHENG, Ying LIU, Huifeng JIANG, Xiaoxian GUO
    2020, 1(6):  697-708.  doi:10.12211/2096-8280.2020-034
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    DNA is the primary carrier of genetic information in various types of life forms. DNA synthesis is a technology that enables the de novo generation of a blueprint for biological functions. It is one of the key generic technologies in many areas of life sciences and the fundamental tool of biotechnology revolution. Distinct from conventional genetic engineering technologies that can only modify natural DNA, DNA synthesis technologies allow limitless creativity for build of designed nucleotide sequence, rewriting of the organism's genetic information as well as creation of synthetic genomes. Advancements in DNA synthesis have led to remarkable improvements in our ability to understand and engineer biological systems. The process of synthetic creation of DNA involves synthesis of oligonucleotide, assembly of multiple constructs together into longer DNA pieces and the associated error-correction procedures to reduce errors produced during oligo synthesis and subsequent assembly. Here, we review current advancements as well as some of the challenges in the technologies of de novo DNA synthesis, assembly, and error correction. For over six decades, DNA synthesis technologies mainly rely on phosphoramidite chemical synthesis methods which was first invented in the 80s. It has been adopted by both column-based and microarray-based oligo synthesizers. New enzymatic DNA synthesis strategy is poised to revolutionize the field. Despite great potential and recent groundbreaking developments, technical hurdles in enzymatic DNA synthesis methods including blocking technology and protein engineering remain challenging. Due to the limits on length and error rates of the synthesis processes, effective assembly and error correction technologies are required for production of long stretch of DNA. With the rapid development of synthetic biology, there is an urgent and high demand for additional DNA synthesis technologies to produce longer DNA constructs and even complete genomes. Advances in high-throughput, automated, and integrated DNA synthesis technologies will create exponential rates of change in a wide range of fields.

    Yeast terminator engineering: from mechanism exploration to artificial design
    Yue SHENG, Genlin ZHANG
    2020, 1(6):  709-721.  doi:10.12211/2096-8280.2020-009
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    The complexity of biological systems poses challenges for the construction of biological components. The discovery of new control parts and the design of stable and adjustable parts have become one of the important contents of synthetic biology. Acted as a genetic part independently of the coding gene to terminate transcription,a terminator is an important biological part for tuning gene expression when designing synthetic gene networks. The activity of terminator can be strong or weak, thus the choice of terminator will directly affect the amount of mRNA produced. With the gradual clarification of the structure and function on terminator and in-depth analysis of the mechanism of transcription termination, terminator engineering has been rapidly developed to construct shorter, controllable and designable terminators. In this review, the progress about the structural discovery, functional characterization, and transcription termination mechanism of terminator in Saccharomyces cerevisiae are systematically summarized. The artificial design of terminator and its application in the field of fine regulation of pathway engineering are discussed. The challenges and possible solutions for terminator engineering, potential and significance for developing terminator engineering in non-model yeast are also prospected. This review provides a theoretical guidance for researchers to develop synthetic biological elements and optimization of heterologous synthetic pathways.

    An overview on regulatory mechanism of daptomycin biosynthesis
    Jiaole FANG, Zhongyuan LYU, Chenfan SUN, Yifan LIU, Weifeng XU, Xuming MAO, Yongquan LI
    2020, 1(6):  722-731.  doi:10.12211/2096-8280.2020-020
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    Daptomycin is a new cyclic lipopeptide antibiotic, produced by Streptomyces roseosporus, with strong resistance to Gram-positive bacteria. Due to its special manner to block the biosynthesis of peptidoglycan, it is difficult for bacteria to develop resistance to daptomycin. Therefore, daptomycin is also known as the ‘last line of defense’ after vancomycin.After approval of daptomycin for injection (brand name cubicin) used to treat infections caused by some sensitive Gram-positive strains, domestic daptomycin products still mainly rely on imports to keep up with demand. In response to this urgent need, there have been many studies on the structure, physicochemical properties, functional mechanisms and synthesis of daptomycin. The biosynthetic pathway of daptomycin has no typical pathway-specific regulators, suggesting that its synthetic regulation may have a unique mechanism. Based on analysis of daptomycin biosynthetic gene cluster, this article mainly summarizes researches on the regulatory mechanism during daptomycin biosynthesis. Screening and identifying regulatory pathways for daptomycin biosynthesis is of great significance for enriching the secondary metabolic regulation of streptomyces, and will also provide important candidate targets for improving daptomycin production. This review aims to give directions for the targeted transformation to obtain high-yield strains more efficiently, and to provide a theoretical reference for the improved biosynthesis of daptomycin. The regulation of microbial secondary metabolism can be divided into three levels, namely global regulation, pleiotropic regulation and pathway-specific regulation. Through analyzing and constructing a regulatory network for the synthesis of secondary metabolites, we can see the key targets of genetic transformation and provide an entry point for high-yield strategies for secondary metabolism, thereby helping us to more effectively carry out targeted high-yield transformation of bacteria and increase the yield of metabolites. With the identifications of gene functions in the daptomycin synthesis gene cluster and the clarification of the daptomycin biosynthesis regulatory network, more genetically targeted transformation and breeding optimization methods have emerged. At the same time, with the development and optimization of the fermentation process, the goal of greatly increasing production of daptomycin biosynthesis in China can be achieved.