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Synthetically engineered microbes reveal interesting principles of cooperation
Michael D. Dressler,Corey J. Clark,Chelsea A. Thachettu,Yasmine Zakaria,Omar Tonsi Eldakar,Robert P. Smith
Frontiers of Chemical Science and Engineering. 2017, 11 (1 ): 3-14.
https://doi.org/10.1007/s11705-016-1605-z
Cooperation is ubiquitous in biological systems. However, if natural selection favors traits that confer an advantage to one individual over another, then helping others would be paradoxical. Nevertheless, cooperation persists and is critical in maintaining homeostasis in systems ranging from populations of bacteria to groupings of mammals. Developing an understanding of the dynamics and mechanisms by which cooperation operates is critical in understanding ecological and evolutionary relationships. Over the past decade, synthetic biology has emerged as a powerful tool to study social dynamics. By engineering rationally controlled and modulatable behavior into microbes, we have increased our overall understanding of how cooperation enhances, or conversely constrains, populations. Furthermore, it has increased our understanding of how cooperation is maintained within populations, which may provide a useful framework to influence populations by altering cooperation. As many bacterial pathogens require cooperation to infect the host and survive, the principles developed using synthetic biology offer promise of developing novel tools and strategies to treat infections, which may reduce the use of antimicrobial agents. Overall, the use of engineered cooperative microbes has allowed the field to verify existing, and develop novel, theories that may govern cooperative behaviors at all levels of biology.
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Rhamnolipid synthesis and production with diverse resources
Qingxin Li
Frontiers of Chemical Science and Engineering. 2017, 11 (1 ): 27-36.
https://doi.org/10.1007/s11705-016-1607-x
Rhamnolipids are one of the most effective biosurfactants that are of great interest in industrial applications such as enhancing oil recovery, health care, cosmetics, pharmaceutical processes, food processing, detergents for protein folding, and bioremediation due to their unique characteristics such as low toxicity, surface active property to reduce surface/interfacial tensions, and excellent biodegradability. The genes and metabolic pathways for rhamnolipid synthesis have been well elucidated, but its cost-effective production is still challenging. Pseudomonas aeruginosa , the most powerful rhamnolipid producer, is an opportunistic pathogen, which limits its large scale production and applications. Rhamnolipid production using engineered strains other than Pseudomonas aeruginosa such as E. coli and Pseudomonas putida has received much attention. The highest yield of rhamnolipids is achieved when oil-type carbon sources are used, but using cheaper and renewable carbon sources such as lignocellulose would be an attractive strategy to reduce the production cost of rhamnolipids for various industrial applications.
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Cell surface protein engineering for high-performance whole-cell catalysts
Hajime Nakatani,Katsutoshi Hori
Frontiers of Chemical Science and Engineering. 2017, 11 (1 ): 46-57.
https://doi.org/10.1007/s11705-017-1609-3
Cell surface protein engineering facilitated by accumulation of information on genome and protein structure involves heterologous production and modification of cell surface proteins using genetic engineering, and is important for the development of high-performance whole-cell catalysts. In this field, cell surface display is a major technology by exposing target proteins, such as enzymes, on the cell surface using a carrier protein. The target proteins are fused to the carrier proteins that transport and tether them to the cell surface, as well as to a secretion signal. This paper reviews cell surface display systems for prokaryotic and eukaryotic cells from the perspective of carrier proteins, which determine the number of displayed molecules, and the localization, size, and direction (N- or C- terminal anchoring) of the passengers. We also discuss advanced methods for displaying multiple enzymes and a new method for the immobilization of whole-cell catalysts using adhesive surface proteins.
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Cofactor engineering in cyanobacteria to overcome imbalance between NADPH and NADH: A mini review
Jongmoon Park,Yunnam Choi
Frontiers of Chemical Science and Engineering. 2017, 11 (1 ): 66-71.
https://doi.org/10.1007/s11705-016-1591-1
Cyanobacteria can produce useful renewable fuels and high-value chemicals using sunlight and atmospheric carbon dioxide by photosynthesis. Genetic manipulation has increased the variety of chemicals that cyanobacteria can produce. However, their uniquely abundant NADPH-pool, in other words insufficient supply of NADH, tends to limit their production yields in case of utilizing NADH-dependent enzyme, which is quite common in heterotrophic microbes. To overcome this cofactor imbalance and enhance cyanobacterial fuel and chemical production, various approaches for cofactor engineering have been employed. In this review, we focus on three approaches: (1) utilization of NADPH-dependent enzymes, (2) increasing NADH production, and (3) changing cofactor specificity of NADH-dependent enzymes from NADH to NADPH.
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Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis in Gluconobacter oxydans WSH-003
Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou
Frontiers of Chemical Science and Engineering. 2017, 11 (1 ): 72-88.
https://doi.org/10.1007/s11705-016-1580-4
Pyrroloquinoline quinone (PQQ) plays a significant role as a redox cofactor in combination with dehydrogenases in bacteria. These dehydrogenases play key roles in the oxidation of important substrates for the biotechnology industry, such as vitamin C production. While biosynthesis of PQQ genes has been widely studied, PQQ-transport mechanisms remain unclear. Herein, we used both two-dimensional fluorescence-difference gel electrophoresis tandem mass spectrometry and RNA sequencing to investigate the effects of pqqB overexpression in an industrial strain of Gluconobacter oxydans WSH-003. We have identified 73 differentially expressed proteins and 99 differentially expressed genes, a majority of which are related to oxidation-reduction and transport processes by gene ontology analysis. We also described several putative candidate effectors that responded to increased PQQ levels resulting from pqqB overexpression. Furthermore, quantitative PCR was used to verify five putative PQQ-transport genes among different PQQ producing strains, and the results showed that ompW , B932_1930 and B932_2186 were upregulated in all conditions. Then the three genes were over-expressed in G. oxydans WSH-003 and PQQ production were detected. The results showed that extracellular PQQ of B932_1930 (a transporter) and B932_2186 (an ABC transporter permease) overexpression strains were enhanced by 1.77-fold and 1.67-fold, respectively. The results suggest that the proteins encoded by PqqB, B932_1930 and B932_2186 might enhance the PQQ secretion process.
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Ting Yuan, Yakun Guo, Junkai Dong, Tianyi Li, Tong Zhou, Kaiwen Sun, Mei Zhang, Qingyu Wu, Zhen Xie, Yizhi Cai, Limin Cao, Junbiao Dai
Frontiers of Chemical Science and Engineering. 2017, 11 (1 ): 107-116.
https://doi.org/10.1007/s11705-017-1621-7
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Assembly of biosynthetic pathways in Saccharomyces cerevisiae using a marker recyclable integrative plasmid toolbox
Lidan Ye,Xiaomei Lv,Hongwei Yu
Frontiers of Chemical Science and Engineering. 2017, 11 (1 ): 126-132.
https://doi.org/10.1007/s11705-016-1597-8
A robust and versatile tool for multigene pathway assembly is a key to the biosynthesis of high-value chemicals. Here we report the rapid construction of biosynthetic pathways in Saccharomyces cerevisiae using a marker recyclable integrative toolbox (pUMRI) developed in our research group, which has features of ready-to-use, convenient marker recycling, arbitrary element replacement, shuttle plasmid, auxotrophic marker independence, GAL regulation, and decentralized assembly. Functional isoprenoid biosynthesis pathways containing 4–11 genes with lengths ranging from ~10 to ~22 kb were assembled using this toolbox within 1–5 rounds of reiterative recombination. In combination with GAL-regulated metabolic engineering, high production of isoprenoids (e.g., 16.3 mg?g?1 dcw carotenoids) was achieved. These results demonstrate the wide range of application and the efficiency of the pUMRI toolbox in multigene pathway construction of S. cerevisiae .
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