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Synthetic and Systems Biotechnology

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https://www.readbyqxmd.com/read/29552656/rapid-generation-of-recombinant-pseudomonas-putida-secondary-metabolite-producers-using-ytrex
#1
Andreas Domröse, Robin Weihmann, Stephan Thies, Karl-Erich Jaeger, Thomas Drepper, Anita Loeschcke
Microbial secondary metabolites represent a rich source of valuable compounds with a variety of applications in medicine or agriculture. Effective exploitation of this wealth of chemicals requires the functional expression of the respective biosynthetic genes in amenable heterologous hosts. We have previously established the TREX system which facilitates the transfer, integration and expression of biosynthetic gene clusters in various bacterial hosts. Here, we describe the yTREX system, a new tool adapted for one-step yeast recombinational cloning of gene clusters...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29552655/improving-acarbose-production-and-eliminating-the-by-product-component-c-with-an-efficient-genetic-manipulation-system-of-actinoplanes-sp-se50-110
#2
Qinqin Zhao, Huixin Xie, Yao Peng, Xinran Wang, Linquan Bai
The α-glucosidase inhibitor acarbose is commercially produced by Actinoplanes sp. and used as a potent drug in the treatment of type-2 diabetes. In order to improve the yield of acarbose, an efficient genetic manipulation system for Actinoplanes sp. was established. The conjugation system between E. coli carrying ØC31-derived integrative plasmids and the mycelia of Actinoplanes sp. SE50/110 was optimized by adjusting the parameters of incubation time of mixed culture (mycelia and E. coli ), quantity of recipient cells, donor-to-recipient ratio and the concentration of MgCl2 , which resulted in a high conjugation efficiency of 29...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29552654/rapid-evolution-of-regulatory-element-libraries-for-tunable-transcriptional-and-translational-control-of-gene-expression
#3
Erqing Jin, Lynn Wong, Yun Jiao, Jake Engel, Benjamin Holdridge, Peng Xu
Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29552653/engineering-of-yarrowia-lipolytica-for-production-of-astaxanthin
#4
Kanchana Rueksomtawin Kildegaard, Belén Adiego-Pérez, David Doménech Belda, Jaspreet Kaur Khangura, Carina Holkenbrink, Irina Borodina
Astaxanthin is a red-colored carotenoid, used as food and feed additive. Astaxanthin is mainly produced by chemical synthesis, however, the process is expensive and synthetic astaxanthin is not approved for human consumption. In this study, we engineered the oleaginous yeast Yarrowia lipolytica for de novo production of astaxanthin by fermentation. First, we screened 12 different Y. lipolytica isolates for β-carotene production by introducing two genes for β-carotene biosynthesis: bi-functional phytoene synthase/lycopene cyclase ( crtYB ) and phytoene desaturase ( crtI ) from the red yeast Xanthophyllomyces dendrorhous ...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29552652/a-systems-approach-using-osmac-log-p-and-nmr-fingerprinting-an-approach-to-novelty
#5
Miaomiao Liu, Tanja Grkovic, Xueting Liu, Jianying Han, Lixin Zhang, Ronald J Quinn
The growing number of sequenced microbial genomes has revealed a remarkably large number of secondary metabolite biosynthetic clusters for which the compounds are still unknown. The aim of the present work was to apply a strategy to detect newly induced natural products by cultivating microorganisms in different fermentation conditions. The metabolomic analysis of 4160 fractions generated from 13 actinomycetes under 32 different culture conditions was carried out by1 H NMR spectroscopy and multivariate analysis...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29552651/does-the-eclipse-limit-bacterial-nucleoid-complexity-and-cell-width
#6
REVIEW
Arieh Zaritsky, Avinoam Rabinovitch, Chenli Liu, Conrad L Woldringh
Cell size of bacteria M is related to 3 temporal parameters: chromosome replication time C , period from replication-termination to subsequent division D , and doubling time τ . Steady-state, bacillary cells grow exponentially by extending length L only, but their constant width W is larger at shorter τ 's or longer C 's, in proportion to the number of chromosome replication positions n (= C / τ ), at least in Escherichia coli and Salmonella typhimurium . Extending C by thymine limitation of fast-growing thyA mutants result in continuous increase of M , associated with rising W , up to a limit before branching...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29552650/production-of-anthocyanins-in-metabolically-engineered-microorganisms-current-status-and-perspectives
#7
REVIEW
Jian Zha, Mattheos A G Koffas
Microbial production of plant-derived natural products by engineered microorganisms has achieved great success thanks to large extend to metabolic engineering and synthetic biology. Anthocyanins, the water-soluble colored pigments found in terrestrial plants that are responsible for the red, blue and purple coloration of many flowers and fruits, are extensively used in food and cosmetics industry; however, their current supply heavily relies on complex extraction from plant-based materials. A promising alternative is their sustainable production in metabolically engineered microbes...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29552649/experimental-evolution-and-proximate-mechanisms-in-biology
#8
REVIEW
Xiao Yi
Biological functions - studied by molecular, systems and behavioral biology - are referred to as proximate mechanisms. Why and how they have emerged from the course of evolution are referred to as ultimate mechanisms. Despite the conceptual and technical schism between the disciplines that focus on each, studies from one side can benefit the other. Experimental evolution is an emerging field at the crossroads of functional and evolutionary biology. Herein microorganisms and mammalian cell lines evolve in well-controlled laboratory environments over multiple generations...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29552648/a-review-of-computational-tools-for-design-and-reconstruction-of-metabolic-pathways
#9
REVIEW
Lin Wang, Satyakam Dash, Chiam Yu Ng, Costas D Maranas
Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools...
December 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318204/heterologous-biosynthesis-of-natural-product-naringenin-by-co-culture-engineering
#10
Vijaydev Ganesan, Zhenghong Li, Xiaonan Wang, Haoran Zhang
Co-culture engineering is an emerging approach for microbial biosynthesis of a variety of biochemicals. In this study, E. coli-E. coli co-cultures were developed for heterologous biosynthesis of the natural product naringenin. The co-cultures were composed of two independent E. coli strains dedicated to functional expression of different portions of the biosynthetic pathway, respectively. The co-culture biosynthesis was optimized by investigating the effect of carbon source, E. coli strain selection, timing of IPTG induction and the inoculation ratio between the co-culture strains...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318203/on-monospecific-genera-in-prokaryotic-taxonomy
#11
Guanghong Zuo, Bailin Hao
A monospecific genus contains a single species ever since it was proposed. Though formally more than half of the known prokaryotic genera are monospecific, we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides. Taking monophyly as a guiding principle, our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes, as provided by the LVTree Viewer and CVTree Web Server, respectively. The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318202/fundamental-crispr-cas9-tools-and-current-applications-in-microbial-systems
#12
REVIEW
Pingfang Tian, Jia Wang, Xiaolin Shen, Justin Forrest Rey, Qipeng Yuan, Yajun Yan
Derived from the bacterial adaptive immune system, CRISPR technology has revolutionized conventional genetic engineering methods and unprecedentedly facilitated strain engineering. In this review, we outline the fundamental CRISPR tools that have been employed for strain optimization. These tools include CRISPR editing, CRISPR interference, CRISPR activation and protein imaging. To further characterize the CRISPR technology, we present current applications of these tools in microbial systems, including model- and non-model industrial microorganisms...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318201/protein-engineering-of-oxidoreductases-utilizing-nicotinamide-based-coenzymes-with-applications-in-synthetic-biology
#13
REVIEW
Chun You, Rui Huang, Xinlei Wei, Zhiguang Zhu, Yi-Heng Percival Zhang
Two natural nicotinamide-based coenzymes (NAD and NADP) are indispensably required by the vast majority of oxidoreductases for catabolism and anabolism, respectively. Most NAD(P)-dependent oxidoreductases prefer one coenzyme as an electron acceptor or donor to the other depending on their different metabolic roles. This coenzyme preference associated with coenzyme imbalance presents some challenges for the construction of high-efficiency in vivo and in vitro synthetic biology pathways. Changing the coenzyme preference of NAD(P)-dependent oxidoreductases is an important area of protein engineering, which is closely related to product-oriented synthetic biology projects...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318200/genome-and-metabolic-engineering-in-non-conventional-yeasts-current-advances-and-applications
#14
REVIEW
Ann-Kathrin Löbs, Cory Schwartz, Ian Wheeldon
Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisia e is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318199/engineering-bacteria-for-enhanced-polyhydroxyalkanoates-pha-biosynthesis
#15
REVIEW
Guo-Qiang Chen, Xiao-Ran Jiang
Polyhydroxyalkanoates (PHA) have been produced by some bacteria as bioplastics for many years. Yet their commercialization is still on the way. A few issues are related to the difficulty of PHA commercialization: namely, high cost and instabilities on molecular weights (Mw) and structures, thus instability on thermo-mechanical properties. The high cost is the result of complicated bioprocessing associated with sterilization, low conversion of carbon substrates to PHA products, and slow growth of microorganisms as well as difficulty of downstream separation...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318198/transcription-control-engineering-and-applications-in-synthetic-biology
#16
REVIEW
Michael D Engstrom, Brian F Pfleger
In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein), a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity) levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318197/metabolic-engineering-for-the-microbial-production-of-isoprenoids-carotenoids-and-isoprenoid-based-biofuels
#17
REVIEW
Fu-Xing Niu, Qian Lu, Yi-Fan Bu, Jian-Zhong Liu
Isoprenoids are the most abundant and highly diverse group of natural products. Many isoprenoids have been used for pharmaceuticals, nutraceuticals, flavors, cosmetics, food additives and biofuels. Carotenoids and isoprenoid-based biofuels are two classes of important isoprenoids. These isoprenoids have been produced microbially through metabolic engineering and synthetic biology efforts. Herein, we briefly review the engineered biosynthetic pathways in well-characterized microbial systems for the production of carotenoids and several isoprenoid-based biofuels...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29318196/engineered-polyketides-synergy-between-protein-and-host-level-engineering
#18
REVIEW
Jesus F Barajas, Jacquelyn M Blake-Hedges, Constance B Bailey, Samuel Curran, Jay D Keasling
Metabolic engineering efforts toward rewiring metabolism of cells to produce new compounds often require the utilization of non-native enzymatic machinery that is capable of producing a broad range of chemical functionalities. Polyketides encompass one of the largest classes of chemically diverse natural products. With thousands of known polyketides, modular polyketide synthases (PKSs) share a particularly attractive biosynthetic logic for generating chemical diversity. The engineering of modular PKSs could open access to the deliberate production of both existing and novel compounds...
September 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29062971/characterization-of-the-metallo-dependent-amidohydrolases-responsible-for-auxiliary-leucinyl-removal-in-the-biosynthesis-of-2-2-bipyridine-antibiotics
#19
Ming Chen, Bo Pang, Ya-Nan Du, Yi-Peng Zhang, Wen Liu
2,2'-Bipyridine (2,2'-BiPy) is an attractive core structure present in a number of biologically active natural products, including the structurally related antibiotics caerulomycins (CAEs) and collismycins (COLs). Their biosynthetic pathways share a similar key 2,2'-BiPy-l-leucine intermediate, which is desulfurated or sulfurated at C5, arises from a polyketide synthase/nonribosomal peptide synthetase hybrid assembly line. Focusing on the common off-line modification steps, we here report that the removal of the "auxiliary" l-leucine residue relies on the metallo-dependent amidohydrolase activity of CaeD or ColD...
June 2017: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29062970/improvement-of-pristinamycin-i-pi-production-in-streptomyces-pristinaespiralis-by-metabolic-engineering-approaches
#20
Jiali Meng, Rongrong Feng, Guosong Zheng, Mei Ge, Yvonne Mast, Wolfgang Wohlleben, Jufang Gao, Weihong Jiang, Yinhua Lu
Pristinamycin, produced by Streptomyces pristinaespiralis , which is a streptogramin-like antibiotic consisting of two chemically unrelated components: pristinamycin I (PI) and pristinamycin II (PII), shows potent activity against many antibiotic-resistant pathogens. However, so far pristinamycin production titers are still quite low, particularly those of PI. In this study, we constructed a PI single component producing strain by deleting the PII biosynthetic genes ( snaE1 and snaE2 ). Then, two metabolic engineering approaches, including deletion of the repressor gene papR3 and chromosomal integration of an extra copy of the PI biosynthetic gene cluster (BGC), were employed to improve PI production...
June 2017: Synthetic and Systems Biotechnology
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