A growth‐rate composition formula for the growth of E. coli on co‐utilized carbon substrates

When bacteria are cultured in medium with multiple carbon substrates, they frequently consume these substrates simultaneously. Building on recent advances in the understanding of metabolic coordination exhibited by Escherichia coli cells through cAMP‐Crp signaling, we show that this signaling system responds to the total carbon‐uptake flux when substrates are co‐utilized and derive a mathematical formula that accurately predicts the resulting growth rate, based only on the growth rates on individual substrates.     

Co‐hydrolysis of lignocellulosic biomass for microbial lipid accumulation

The herbaceous perennial energy crops miscanthus, giant reed, and switchgrass, along with the annual crop residue corn stover, were evaluated for their bioconversion potential. A co‐hydrolysis process, which applied dilute acid pretreatment, directly followed by enzymatic saccharification without detoxification and liquid–solid separation between these two steps was implemented to convert lignocellulose into monomeric sugars (glucose and xylose). A factorial experiment in a randomized block design was employed to optimize the co‐hydrolysis process. Under the optimal reaction conditions, corn stover exhibited the greatest total sugar yield (glucose + xylose) at 0.545 g g^?1 dry biomass at 83.3% of the theoretical yield, followed by switch grass (0.44 g g^?1 dry biomass, 65.8% of theoretical yield), giant reed (0.355 g g^?1 dry biomass, 64.7% of theoretical yield), and miscanthus (0.349 g g^?1 dry biomass, 58.1% of theoretical yield). The influence of combined severity factor on the susceptibility of pretreated substrates to enzymatic hydrolysis was clearly discernible, showing that co‐hydrolysis is a technically feasible approach to release sugars from lignocellulosic biomass. The oleaginous fungus Mortierella isabellina was selected and applied to the co‐hydrolysate mediums to accumulate fungal lipids due to its capability of utilizing both C5 and C6 sugars. Fungal cultivations grown on the co‐hydrolysates exhibited comparable cell mass and lipid production to the synthetic medium with pure glucose and xylose. These results elucidated that combining fungal fermentation and co‐hydrolysis to accumulate lipids could have the potential to enhance the utilization efficiency of lignocellulosic biomass for advanced biofuels production. Biotechnol. Bioeng. 2013; 110: 1039–1049. © 2012 Wiley Periodicals, Inc.     

果糖和麦芽糖作为有氧碳源对大肠杆菌NZN111两阶段发酵中厌氧发酵的影响

为了了解磷酸转移酶转运系统 (PTS) 依赖和非PTS依赖代谢的糖类对大肠杆菌生产琥珀酸的影响,进行了两阶段培养,有氧阶段采用PTS依赖型的果糖或非PTS依赖型的麦芽糖作为丙酮酸甲酸裂解酶 (PFL) 和乳酸脱氢酶 (LDH) 双突变株NZN111的碳源,研究其对NZN111厌氧阶段代谢葡萄糖的影响。5 L罐发酵结果表明,以果糖和麦芽糖为碳源有氧培养的细胞恢复了在厌氧条件下快速代谢葡萄糖的能力,琥珀酸和丙酮酸成为主要代谢产物,最终琥珀酸得率分别为0.84和0.75 mol/mol,丙酮酸得率分别达到了0.65和0.83 mol/mol,琥珀酸和丙酮酸终浓度比分别为1.73∶1和1.21∶1。果糖和麦芽糖培养的NZN111与葡萄糖培养的菌体代谢的明显差异推测是cyclic AMP (cAMP) 依赖型和非cAMP依赖型的分解代谢物阻遏调控这两种机制共同作用的结果。     

Constructing E. coli Co‐Cultures for De Novo Biosynthesis of Natural Product Acacetin

Modular co‐culture engineering is an emerging approach for biosynthesis of complex natural products. In this study, microbial co‐cultures composed of two and three Escherichia coli strains, respectively, are constructed for de novo biosynthesis of flavonoid acacetin, a value‐added natural compound possessing numerous demonstrated biological activities, from simple carbon substrate glucose. To this end, the heterologous biosynthetic pathway is divided into different modules, each of which is accommodated in a dedicated E. coli strain for functional expression. After the optimization of the inoculation ratio between the constituent strains, the engineered co‐cultures show a 4.83‐fold improvement in production comparing to the mono‐culture controls. Importantly, cultivation of the three‐strain co‐culture in shake flasks result in the production of 20.3 mg L^?1 acacetin after 48 h. To the authors' knowledge, this is the first report on acacetin de novo biosynthesis in a heterologous microbial host. The results of this work confirm the effectiveness of modular co‐culture engineering for complex flavonoid biosynthesis.     

Synthesis of alkaline protease by catabolite repression- resistant Thermoactinomyces sp. E79 mutant

The production of alkaline protease from Thermoactinomyces sp. E79 was repressed by 0.2% (w/v) glucose in the medium. Catabolite repression-resistant mutant M1 was obtained by combined treatment of UV light and N-methyl- N-nitro-N-nitrosoguanidine. The glucose uptake studies accomplished by [14C]glucose showed that the mutant has lost its ability for glucose uptake. The protease production by mutant M1 in the enzyme production medium was 62 U/mg, which was twice that of the wild-type strain.     

Molecular mechanisms controlling fructose‐specific memory and catabolite repression in lactose metabolism by Streptococcus mutans

Lactose is an abundant dietary carbohydrate metabolized by the dental pathogen Streptococcus mutans. Lactose metabolism presents both classic diauxic behaviors and long‐term memory, where the bacteria can pause for >11 h before initiating growth on lactose. Here, we explored mechanisms contributing to unusual aspects of regulation of the lac operon. The fructose‐phosphate metabolites, F‐1‐P and F‐6‐P, could modulate the DNA‐binding activities of the lactose repressor. Recombinant LacR proteins bound upstream of lacA and Gal‐6‐P induced the formation of different LacR‐DNA complexes. Deletion of lacR resulted in strain‐specific growth phenotypes on lactose, but also on a number of mono‐ and di‐saccharides that involve the glucose‐PTS or glucokinase in their catabolism. The phenotypes were consistent with the novel findings that loss of LacR altered glucose‐PTS activity and expression of the gene for glucokinase. CcpA was also shown to affect lactose metabolism in vivo and to bind to the lacA promoter region in vitro. Collectively, our study reveals complex molecular circuits controlling lactose metabolism in S. mutans, where LacR and CcpA integrate cellular and environmental cues to regulate metabolism of a variety of carbohydrates that are critical to persistence and pathogenicity of S. mutans.     

Microbial degradation and physico-chemical alteration of polyhydroxyalkanoates by a thermophilic <Emphasis Type="Italic">Streptomyces</Emphasis> sp.

A thermophilic Streptomyces sp. capable of degrading various aliphatic polyesters was isolated from a landfill site. The isolate, Streptomyces sp. BCC23167, demonstrated rapid aerobic degradation of several polyesters, including polyhydroxyalkanoate copolymers, poly(ɛ-caprolactone) and polybutylene succinate at 50°C and neutral pH. The degrading activity was repressed by glucose and cellobiose, but tolerant to repression by other carbon substrates. Degradation of a commercial poly[(R)-3-hydroxybutyrate-co-3-hydroxyhexanoate] (PHBHx) by Streptomyces sp. BCC23167 progressed from surface to bulk as suggested by the slight decrease in polymer molecular weight. Differential scanning calorimetry analysis of PHBHx film degradation by Streptomyces sp. BCC23167 showed that relative crystallinity of the film increased slightly in the early stage of degradation, followed by a marked decrease later on. The surface morphology of degraded films was analyzed by scanning electron microscopy, which showed altered surface structure consistent with the changes in crystallinity. The isolate is thus of potential for application in composting technology for bio-plastic degradation.     

敲除MIG1和SNF1基因对酿酒酵母共利用葡萄糖和木糖的影响

Mig1和Snf1是酿酒酵母葡萄糖阻遏效应的两个关键调控因子。为了提高酿酒酵母工程菌同时利用葡萄糖和木糖的能力,分别对MIG1和SNF1基因进行了单敲除和双敲除,并通过摇瓶发酵实验和RNA-Seq转录组分析,初步揭示了Mig1和Snf1可能影响葡萄糖和木糖共利用表达差异基因的层级调控机制。研究结果表明,MIG1单敲除对混合糖的共利用影响不大;SNF1单敲除会加快混合糖中木糖的利用而且葡萄糖和木糖可以被同时利用,这可能归因于SNF1单敲除会解除对一些氮分解代谢阻遏基因表达的抑制,从而促进了细胞对氮源营养的利用;进一步敲除MIG1,会解除更多氮分解代谢阻遏基因表达的抑制,以及一些碳中心代谢途径基因表达上调。虽然MIG1和SNF1双敲除菌株利用葡萄糖加快而利用木糖变慢,但是葡萄糖和木糖可以被同时利用,进而加快乙醇的积累。综上所述,MIG1和SNF1的敲除导致氮分解阻遏基因表达上调,有助于促进葡萄糖和木糖的共利用;解析Mig1和Snf1对氮分解阻遏基因的层级调控作用,为进一步提高葡萄糖和木糖的共利用提供新的靶点。     

Synthetic mutualism in engineered E. coli mutant strains as functional basis for microbial production consortia

In nature, microorganisms often reside in symbiotic co-existence providing nutrition, stability, and protection for each partner by applying “division of labor.” This principle may also be used for the overproduction of targeted compounds in bioprocesses. It requires the engineering of a synthetic co-culture with distributed tasks for each partner. Thereby, the competition on precursors, redox cofactors, and energy—which occurs in a single host—is prevented. Current applications often focus on unidirectional interactions, that is, the product of partner A is used for the completion of biosynthesis by partner B. Here, we present a synthetically engineered Escherichia coli co-culture of two engineered mutant strains marked by the essential interaction of the partners which is achieved by implemented auxotrophies. The tryptophan auxotrophic strain E. coli ANT-3, only requiring small amounts of the aromatic amino acid, provides the auxotrophic anthranilate for the tryptophan producer E. coli TRP-3. The latter produces a surplus of tryptophan which is used to showcase the suitability of the co-culture to access related products in future applications. Co-culture characterization revealed that the microbial consortium is remarkably functionally stable for a broad range of inoculation ratios. The range of robust and functional interaction may even be extended by proper glucose feeding which was shown in a two-compartment bioreactor setting with filtrate exchange. This system even enables the use of the co-culture in a parallel two-level temperature setting which opens the door to access temperature sensitive products via heterologous production in E. coli in a continuous manner.     

酿酒酵母戊糖转运蛋白及C6/C5共代谢菌株的研究进展

充分利用木质纤维素中的糖分是提高以此类生物质为原料生产二代燃料乙醇经济盈利性的基本要求,也是实现其他生物基化学品规模化生产的基础。传统的乙醇生产微生物酿酒酵母Saccharomyces cerevisiae具有独特的生产性能及内在优势,是备受关注的底盘细胞,但其不能有效地利用戊糖。利用代谢工程、合成生物学策略,对二代燃料乙醇生产专用酿酒酵母的精准构制持续研究了30余年,已明显改善了其对木糖/葡萄糖的乙醇共发酵能力。近年来关注点集中在早期忽略的限速步骤即糖转运环节的研究上,以期实现不同糖分各行其道、高效专一性转运蛋白各行其责的二代燃料乙醇生产特种酿酒酵母所需的糖转运理想状态。文中主要综述了酿酒酵母戊糖转运蛋白的研究进展,及酿酒酵母的木糖和L-阿拉伯糖代谢工程的研究现状。     

Co‐culture engineering for microbial biosynthesis of 3‐amino‐benzoic acid in Escherichia coli

3‐amino‐benzoic acid (3AB) is an important building block molecule for production of a wide range of important compounds such as natural products with various biological activities. In the present study, we established a microbial biosynthetic system for de novo 3AB production from the simple substrate glucose. First, the active 3AB biosynthetic pathway was reconstituted in the bacterium Escherichia coli, which resulted in the production of 1.5 mg/L 3AB. In an effort to improve the production, an E. coli‐E. coli co‐culture system was engineered to modularize the biosynthetic pathway between an upstream strain and an downstream strain. Specifically, the upstream biosynthetic module was contained in a fixed E. coli strain, whereas a series of E. coli strains were engineered to accommodate the downstream biosynthetic module and screened for optimal production performance. The best co‐culture system was found to improve 3AB production by 15 fold, compared to the mono‐culture approach. Further engineering of the co‐culture system resulted in biosynthesis of 48 mg/L 3AB. Our results demonstrate co‐culture engineering can be a powerful new approach in the broad field of metabolic engineering.     

Expression of recombinant protein A from the lac promoter in Escherichia coli JM83 is not subject to catabolite repression when grown under specific conditions of continuous culture

Although widely used in experimental and industrial situations, genetically engineered plasmids containing the lac promoter from Escherichia coli are subject to catabolite repression when grown in glucose-containing media. Several methods of overcoming this problem have been investigated by studying the expression of the protein A gene from Staphylococcus aureus under the control of the Escherichia coli lac promoter. When glycerol is used as a sole carbon source, the plasmid is unstable and is rapidly lost from the culture. When the bacteria are grown in chemostats under glucose limitation, the plasmid is maintained, even at high dilution rates, and the expression of protein A is similar to that observed when glycerol was used. The balance between metabolic load and protein A expression seems to be maintained by reducing the gene dose to a tolerable level. Depending on the metabolic conditions prevailing in the culture, this is achieved, either by reducing the copy number of the plasmid or in extreme cases by removing the plasmid altogether.     

大肠杆菌tktA基因的克隆表达

tktA是芳香族氨基酸生物合成共同途径的关键酶基因之一,在大肠杆菌中,tktA编码转酮酶A,在磷酸戊糖途径生成4－磷酸赤藓糖中起主要作用。采用PCR方法从大肠杆菌K－12株中扩增到tktA,并实现了高效表达,tktA活性提高了3．9倍,并且使芳香族氨基酸生物合成共同途径中关键中间产物DAHP的产量有所提高。     

Biosynthesis of geranate via isopentenol utilization pathway in Escherichia coli

Isoprenoids are a large family of natural products with diverse structures, which allow them to play diverse and important roles in the physiology of plants and animals. They also have important commercial uses as pharmaceuticals, flavoring agents, fragrances, and nutritional supplements. Recently, metabolic engineering has been intensively investigated and emerged as the technology of choice for the production of isoprenoids through microbial fermentation. Isoprenoid biosynthesis typically originates in plants from acetyl-coA in central carbon metabolism, however, a recent study reported an alternative pathway, the isopentenol utilization pathway (IUP), that can provide the building blocks of isoprenoid biosynthesis from affordable C5 substrates. In this study, we expressed the IUP in Escherichia coli to efficiently convert isopentenols into geranate, a valuable isoprenoid compound. We first established a geraniol-producing strain in E. coli that uses the IUP. Then, we extended the geraniol synthesis pathway to produce geranate through two oxidation reactions catalyzed by two alcohol/aldehyde dehydrogenases from Castellaniella defragrans. The geranate titer was further increased by optimizing the expression of the two dehydrogenases and also parameters of the fermentation process. The best strain produced 764 mg/L geranate in 24 h from 2 g/L isopentenols (a mixture of isoprenol and prenol). We also investigated if the dehydrogenases could accept other isoprenoid alcohols as substrates.