Abstract:
:2-Pyrone-4,6-dicarboxylic acid (PDC) is a pseudoaromatic dicarboxylic acid and is a promising biobased building block chemical that can be used to make diverse polyesters with novel functionalities. In this study, Escherichia coli was metabolically engineered to produce PDC from glucose. First, an efficient biosynthetic pathway for PDC production from glucose was suggested by in silico metabolic flux simulation. This best pathway employs a single-step biosynthetic route to protocatechuic acid (PCA), a metabolic precursor for PDC biosynthesis. On the basis of the selected PDC biosynthetic pathway, a shikimate dehydrogenase (encoded by aroE)-deficient E. coli strain was engineered by introducing heterologous genes of different microbial origin encoding enzymes responsible for converting 3-dehydroshikimate (DHS) to PDC, which allowed de novo biosynthesis of PDC from glucose. Next, production of PDC was further improved by applying stepwise rational metabolic engineering strategies. These include elimination of feedback inhibition on 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (encoded by aroG) by overexpressing a feedback-resistant variant, enhancement of the precursor phosphoenolpyruvate supply by changing the native promoter of the ppsA gene with the strong trc promoter, and reducing accumulation of the major byproduct DHS by overexpression of a DHS importer (encoded by shiA). Furthermore, cofactor (NADP+/NADPH) utilization was manipulated through genetic modifications of the E. coli soluble pyridine nucleotide transhydrogenase (encoded by sthA), and the resultant impact on PDC production was investigated. Fed-batch fermentation of the final engineered E. coli strain allowed production of 16.72 g/L of PDC from glucose with the yield and productivity of 0.201 g/g and 0.172 g/L/h, respectively, representing the highest PDC production performance indices reported to date.
journal_name
ACS Synth Bioljournal_title
ACS synthetic biologyauthors
Luo ZW,Kim WJ,Lee SYdoi
10.1021/acssynbio.8b00281subject
Has Abstractpub_date
2018-09-21 00:00:00pages
2296-2307issue
9issn
2161-5063journal_volume
7pub_type
杂志文章abstract::We have previously engineered green/red and red/far red photoreversible E. coli phytochrome and cyanobacteriochrome (CBCR) two-component systems (TCSs) and utilized them to program tailor-made gene expression signals for gene circuit characterization. Here, we transport the UV-violet/green photoreversible CBCR TCS Uir...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00068
更新日期:2016-07-15 00:00:00
abstract::To spatially control biochemical functions at specific sites within a genome, we have engineered a synthetic switch that activates when bound to its DNA target site. The system uses two CRISPR-Cas complexes to colocalize components of a de novo-designed protein switch (Co-LOCKR) to adjacent sites in the genome. Coloca...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00012
更新日期:2020-09-18 00:00:00
abstract::The cellular response to hypoxia is orchestrated by HIF-1, a heterodimeric transcription factor composed of an α and a β subunit that enables cell survival under low oxygen conditions by altering the transcription of over 300 genes. There is significant evidence that inhibition of HIF-1 would be beneficial for cancer ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00219
更新日期:2017-03-17 00:00:00
abstract::RNA structures regulate various steps in gene expression. Transcription in bacteria is typically terminated by stable hairpin structures. Translation initiation can be modulated by metabolite- or temperature-sensitive RNA structures, called riboswitches or RNA thermometers (RNATs), respectively. RNATs control translat...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.7b00356
更新日期:2018-02-16 00:00:00
abstract::The structural complexity of nonribosomal peptides (NRPs) impeding economic chemical synthesis and poor cultivability of source organisms limits the development of bioprocesses for novel bioactive compounds. Since nonribosomal peptide synthetases (NRPSs) assemble NRPs from simple amino acid building blocks, heterologo...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/sb400082j
更新日期:2014-07-18 00:00:00
abstract::Amyloids are highly ordered, hierarchal protein nanoassemblies. Functional amyloids in bacterial biofilms, such as Escherichia coli curli fibers, are formed by the polymerization of monomeric proteins secreted into the extracellular space. Curli is synthesized by living cells, is primarily composed of the major curlin...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00166
更新日期:2017-02-17 00:00:00
abstract::In the search for enzymatically processed RNA fragments, we found the novel three-way junction motif. The structure prediction suggested the arrangement of helices at acute angle approx. 60°. This allows the design of a trimeric RNA nanoparticle that can be functionalized with multiple regulatory fragments. Such RNA n...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.8b00319
更新日期:2019-03-15 00:00:00
abstract::A defining goal of synthetic biology is to develop biomaterials with superior performance and versatility. Here we introduce a purely genetically encoded and self-assembling biopolymer based on the SpyTag-SpyCatcher chemistry. We show the application of this polymer for highly efficient uranyl binding and extraction f...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.8b00223
更新日期:2018-10-19 00:00:00
abstract::Transcription activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria to aid the infection of plant species. TALEs assist infections by binding to specific DNA sequences and activating the expression of host genes. Recent results show that TALE proteins consist of a central repeat domain, which ...
journal_title:ACS synthetic biology
pub_type: 杂志文章,评审
doi:10.1021/sb400137b
更新日期:2014-10-17 00:00:00
abstract::Due to autotrophic growing capacity and extremely rich secondary metabolism, plants should be preferred targets of synthetic biology. However, developments in plants usually run below those in other taxonomic groups. In this work we engineered genetic circuits capable of logic YES, OR and AND Boolean computation in pl...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.8b00214
更新日期:2018-10-19 00:00:00
abstract::To program cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, in practice, modulating gene expression is widely carried out using prototypical ligand-inducible promoters, which have limited tunability and spatiotemporal resolution. ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.8b00280
更新日期:2018-11-16 00:00:00
abstract::In this work, we develop methodologies for analyzing and cross comparing metabolic models. We investigate three important metabolic networks to discuss the complexity of biological organization of organisms, modeling, and system properties. In particular, we analyze these metabolic networks because of their biotechnol...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/sb300102k
更新日期:2013-05-17 00:00:00
abstract::Cell-free systems provide a versatile platform for the development of low-cost, easy-to-use sensors for diverse analytes. However, sensor affinity dictates response sensitivity, and improving binding affinity can be challenging. Here, we describe efforts to address this problem while developing a biosensor for vitamin...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00429
更新日期:2020-02-21 00:00:00
abstract::We recently developed a technique for rapidly and reversibly inhibiting protein function through light-inducible sequestration of proteins away from their normal sites of action. Here, we adapt this method for inducible inactivation of Bem1, a scaffold protein involved in budding yeast polarity. We find that acute inh...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.5b00053
更新日期:2015-10-16 00:00:00
abstract::Carotenoids, a variety of natural products, have significant pharmaceutical and commercial potential. Phytoene dehydrogenase (CrtI) is the rate-limit enzyme for carotenoid synthesis, whose catalysis specificity results in various carotenoids. However, the structural characteristics of CrtI for controlling the catalysi...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00128
更新日期:2020-07-17 00:00:00
abstract::Transform-MinER (Transforming Molecules in Enzyme Reactions) is a web application facilitating the exploration of chemical biosynthetic space, guiding the user toward promising start points for enzyme design projects or directed evolution experiments. Two types of search are possible: Molecule Search allows a user to ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00105
更新日期:2019-11-15 00:00:00
abstract::Cellobiose phosphorylase (CBP) cleaves cellobiose-abundant in plant biomass-to glucose and glucose 1-phosphate. However, the pentose sugar xylose, also abundant in plant biomass, acts as a mixed-inhibitor and a substrate for the reverse reaction, limiting the industrial potential of CBP. Preventing xylose, which lacks...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00211
更新日期:2017-02-17 00:00:00
abstract::We present the OpenPlant toolkit, a set of interlinked resources and techniques to develop Marchantia as testbed for bioengineering in plants. Marchantia is a liverwort, a simple plant with an open form of development that allows direct visualization of gene expression and dynamics of cellular growth in living tissues...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00511
更新日期:2020-04-17 00:00:00
abstract::We developed a hybrid synthetic circuit that co-opts the genetic regulation of the native bacterial quorum sensing autoinducer-2 and imposes an extra external controller for maintaining tightly controlled gene expression. This dual-input genetic controller was mathematically modeled and, by design, can be operated in ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00179
更新日期:2020-10-16 00:00:00
abstract::Gene expression noise arises from stochastic variation in the synthesis and degradation of mRNA and protein molecules and creates differences in protein numbers across populations of genetically identical cells. Such variability can lead to imprecision and reduced performance of both native and synthetic networks. In ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.8b00279
更新日期:2018-11-16 00:00:00
abstract::Komagataeibacter xylinus has received increasing attention as an important microorganism for the conversion of several carbon sources to bacterial cellulose (BC). However, BC productivity has been impeded by the lack of efficient genetic engineering techniques. In this study, a lambda Red and FLP/FRT-mediated site-spe...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00450
更新日期:2020-11-20 00:00:00
abstract::Synthetic biology is today harnessing the design of novel and greener biosynthesis routes for the production of added-value chemicals and natural products. The design of novel pathways often requires a detailed selection of enzyme sequences to import into the chassis at each of the reaction steps. To address such desi...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.5b00294
更新日期:2016-06-17 00:00:00
abstract::A major force shaping form and patterns in biology is based in the presence of amplification mechanisms able to generate ordered, large-scale spatial structures out of local interactions and random initial conditions. Turing patterns are one of the best known candidates for such ordering dynamics, and their existence ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.5b00254
更新日期:2016-07-15 00:00:00
abstract::Constructing efficient cellular factories often requires integration of heterologous pathways for synthesis of novel compounds and improved cellular productivity. Few genomic sites are routinely used, however, for efficient integration and expression of heterologous genes, especially in nonmodel hosts. Here, a data-gu...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00299
更新日期:2020-09-18 00:00:00
abstract::Synthetic biology and metabolic engineering offer potentially green and attractive routes to the production of high value compounds. The provision of high-quality parts and pathways is crucial in enabling the biosynthesis of chemicals using synthetic biology. While a number of regulatory parts that provide control at ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00375
更新日期:2020-10-16 00:00:00
abstract::Metabolic engineering of Escherichia coli was performed to construct a 100% rationally engineered strain capable of overproducing L-isoleucine, an important branched-chain amino acid. The thrABC (encoding L-threonine biosynthetic enzymes), ilvA (encoding feedback-resistant threonine dehydratase), ilvIH (encoding feedb...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/sb300071a
更新日期:2012-11-16 00:00:00
abstract::Cell-free gene expression systems are emerging as an important platform for a diverse range of synthetic biology and biotechnology applications, including production of robust field-ready biosensors. Here, we combine programmed cellular autolysis with a freeze-thaw or freeze-dry cycle to create a practical, reproducib...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.7b00253
更新日期:2017-12-15 00:00:00
abstract::As a product of a multistep enzymatic reaction, accumulation of poly(3-hydroxybutyrate) (PHB) in Escherichia coli (E. coli) can be achieved by overexpression of the PHB synthesis pathway from a native producer involving three genes phbC, phbA, and phbB. Pathway optimization by adjusting expression levels of the three ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00083
更新日期:2016-11-18 00:00:00
abstract::Characterization of genetic control elements is essential for the predictable engineering of synthetic biology systems. The current standard for in vivo characterization of control elements is through the use of fluorescent reporter proteins such as green fluorescent protein (GFP). Gene expression, however, involves n...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/sb400089c
更新日期:2014-03-21 00:00:00
abstract::Noncanonical amino acids form a highly diverse pool of building blocks that can render unique physicochemical properties to peptides and proteins. Here, four methionine analogues with unsaturated and varying side chain lengths were successfully incorporated at four different positions in nisin in Lactococcus lactis th...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00308
更新日期:2020-09-18 00:00:00