Adaptive evolution improves acid tolerance and succinic acid production in Actinobacillus succinogenes

Fermentation at low pH is an efficient way to improve the competitiveness of biological succinic acid-producing process. Actinobacillus succinogenes shows good performance of succinic acid production under anaerobic conditions, but its succinic acid production capability at the low-pH is inefficient due to the poor acid resistance. Herein, a mutant A. succinogenes BC-4 with improved cell growth and succinic acid production under weak acid conditions was obtained by adaptive evolution. The specific growth rate and succinic acid production of BC-4 reached 0.13 g/L/h and 20.77 g/L, which were increased by 3.25- and 2.95- fold, respectively compared with the parent strain under anaerobic condition at pH 5.8. The activities of specific enzymes with ATP generation were significantly enhanced under weak acidic conditions, resulting in 1.28-fold increase in the maximum ATP level. Membrane fatty acid composition analysis demonstrated that the ratio of saturated to unsaturated fatty acids was decreased from 1.62 to 1.44 in mutant BC-4, leading to improved intracellular pH homeostasis. Furthermore, the change from long-chain to median-chain fatty acid might lower the permeability of H⁺ into cytoplasm for survival under acid stress. These results indicated that A. succinogenes BC-4 is a promising candidate for succinic acid production under weak acid condition.     

Biosensor-assisted evolution for high-level production of 4-hydroxyphenylacetic acid in Escherichia coli

4-Hydroxyphenylacetic acid (4HPAA) is an important building block for synthesizing drugs, agrochemicals, and biochemicals, and requires sustainable production to meet increasing demand. Here, we use a 4HPAA biosensor to overcome the difficulty of conventional library screening in identification of preferred mutants. Strains with higher 4HPAA production and tolerance are successfully obtained by atmospheric and room temperature plasma (ARTP) mutagenesis coupled with adaptive laboratory evolution using this biosensor. Genome shuffling integrates preferred properties in the strain GS-2-4, which produces 25.42 g/L 4HPAA. Chromosomal mutations of the strain GS-2-4 are identified by whole genome sequencing. Through comprehensive analysis and experimental validation, important genes, pathways and regulations are revealed. The best gene combination in inverse engineering, acrD-aroG, increases 4HPAA production of strain GS-2-4 by 37% further. These results emphasize precursor supply and stress resistance are keys to efficient 4HPAA biosynthesis. Our work shows the power of biosensor-assisted screening of mutants from libraries. The methods developed here can be easily adapted to construct cell factories for the production of other aromatic chemicals. Our work also provides many valuable target genes to build cell factories for efficient 4HPAA production in the future.     

适应性进化与甜菜碱的添加促进安丝菌素的生产

【背景】安丝菌素是一类由珍贵束丝放线菌橙色亚种(Actinosynnema pretiosum ssp. auranticu)生产的美登素类衍生抗生素,属于大环内酰胺类物质,根据不同的C-3位基团可以分为一系列衍生物。目前已上市的高效抗癌药物曲妥珠单抗(T-DM1)以AP-3 (Ansamitocin P-3)为生产底物,并表现出很好的乳腺癌治疗效果。然而当前AP-3的产量较低,其过高的成本限制了进一步发展。【目的】应用适应性进化及添加适量甜菜碱策略提高安丝菌素AP-3的产量。【方法】以珍贵束丝放线菌橙色亚种为出发菌株,链霉素和巴龙霉素为胁迫压力进行适应性进化,筛选出安丝菌素积累较高的菌株,随后向进化菌株的发酵培养基中添加0.1%的甜菜碱,AP-3的产量进一步提高,同时分析了进化菌株AP-3相关基因的转录水平,初步探索进化菌株安丝菌素积累提高的原因。【结果】得到2株进化菌株Str16-4-4和Par16-2-1,发酵7d后AP-3产量分别提高了33.4%和31.7%,添加甜菜碱后其AP-3产量相比出发菌株提高了54.6%和47.4%。【结论】通过适应性进化的策略获得了AP-3生产能力提高的珍贵束丝放线菌橙色亚种进化菌株,对促进AP-3的生产提供了新思路,而且为适应性进化策略提高目标产物的产量提供了新的例证。     

Improving the tolerance of Escherichia coli to medium-chain fatty acid production

Microbial fatty acids are an attractive source of precursors for a variety of renewable commodity chemicals such as alkanes, alcohols, and biofuels. Rerouting lipid biosynthesis into free fatty acid production can be toxic, however, due to alterations of membrane lipid composition. Here we find that membrane lipid composition can be altered by the direct incorporation of medium-chain fatty acids into lipids via the Aas pathway in cells expressing the medium-chain thioesterase from Umbellularia californica (BTE). We find that deletion of the aas gene and sequestering exported fatty acids reduces medium-chain fatty acid toxicity, partially restores normal lipid composition, and improves medium-chain fatty acid yields.     

Metabolic engineering of Escherichia coli for production of fatty acid short-chain esters through combination of the fatty acid and 2-keto acid pathways

Fatty acid short-chain esters (FASEs) are biodiesels that are renewable, nontoxic, and biodegradable biofuels. A novel approach for the biosynthesis of FASEs has been developed using metabolically-engineered E. coli through combination of the fatty acid and 2-keto acid pathways. Several genetic engineering strategies were also developed to increase fatty acyl-CoA availability to improve FASEs production. Fed-batch cultivation of the engineered E. coli resulted in a titer of 1008 mg/L FASEs. Since the fatty acid and 2-keto acid pathways are native microbial synthesis pathways, this strategy can be implemented in a variety of microorganisms to produce various FASEs from cheap and readily-available, renewable, raw materials such as sugars and cellulose in the future.     

Adaptive evolution to novel predators facilitates the evolution of damselfly species range shifts

Most species have evolved adaptations to reduce the chances of predation. In many cases, adaptations to coexist with one predator generate tradeoffs in the ability to live with other predators. Consequently, the ability to live with one predator may limit the geographic distributions of species, such that adaptive evolution to coexist with novel predators may facilitate range shifts. In a case study with Enallagma damselflies, we used a comparative phylogenetic approach to test the hypothesis that adaptive evolution to live with a novel predator facilitates range size shifts. Our results suggest that the evolution of Enallagma shifting from living in ancestral lakes with fish as top predators, to living in lakes with dragonflies as predators, may have facilitated an increase in their range sizes. This increased range size likely arose because lakes with dragonflies were widespread, but unavailable as a habitat throughout much of the evolutionary history of Enallagma because they were historically maladapted to coexist with dragonfly predators. Additionally, the traits that have evolved as defenses against dragonflies also likely enhanced damselfly dispersal abilities. While many factors underlie the evolutionary history of species ranges, these results suggest a role for the evolution of predator‐prey interactions.     

Development of an orthogonal fatty acid biosynthesis system in E. coli for oleochemical production

Here we report recombinant expression and activity of several type I fatty acid synthases that can function in parallel with the native Escherichia coli fatty acid synthase. Corynebacterium glutamicum FAS1A was the most active in E. coli and this fatty acid synthase was leveraged to produce oleochemicals including fatty alcohols and methyl ketones. Coexpression of FAS1A with the ACP/CoA-reductase Maqu2220 from Marinobacter aquaeolei shifted the chain length distribution of fatty alcohols produced. Coexpression of FAS1A with FadM, FadB, and an acyl-CoA-oxidase from Micrococcus luteus resulted in the production of methyl ketones, although at a lower level than cells using the native FAS. This work, to our knowledge, is the first example of in vivo function of a heterologous fatty acid synthase in E. coli. Using FAS1 enzymes for oleochemical production have several potential advantages, and further optimization of this system could lead to strains with more efficient conversion to desired products. Finally, functional expression of these large enzyme complexes in E. coli will enable their study without culturing the native organisms.     

Comparative studies of unfolding and binding of ligands to human serum albumin in the presence of fatty acid: spectroscopic approach

This study was undertaken to investigate the influence of fatty acid binding on the unfolding of HSA and how the fatty acid molecules can influence and/or compete with other ligand molecules bound to the protein. The equilibrium unfolding of fatted and fatty acid free HSA was measured by overlapping of unfolding transition curves monitored by different probes for secondary and tertiary structure and determining changes in free energy of unfolding. Proteins stability was studied by fluorescence spectroscopy, whereas conformational changes were detected by circular dichroism techniques. We have suggested a "molten globule" like intermediate state of HSA at a fairly high concentration of GnHCl (3.2 for fatty acid free and 3.6 for fatted). The free energy of stabilization (DeltaG(D)(H2O)) in the presence of fatty acid was found to be 900 cal mol(-1). We also analyze the effects of fatty acid on binding of ligands using spectroscopic technique and reported the equilibrium constants and free energies obtained from the binding and unfolding experiments.     

Modification of the fatty acid specificity of cytochrome P450 BM-3 from Bacillus megaterium by directed evolution: a validated assay

Cytochrome P450 BM-3 (CYP102) catalyzes the subterminal hydroxylation of fatty acids with a chain length of 12–22 carbons. The paper focuses on the regioselectivity and substrate specificity of the purified wild-type enzyme and five mutated variants towards caprylic, capric, and lauric acid. The enzymes were obtained by random mutagenic fine-tuning of the mutant F87A(LARV). F87A(LARV) was selected as the best enzyme variant in a previous study in which the single mutant F87A was subjected to rational evolution to achieve hydroxylation activity for short chain length substrates using a p-nitrophenolate-based spectrophotometric assay.

The best mutants, F87V(LAR) and F87V(LARV), show a higher catalytic activity towards ω-(p-nitrophenoxy)decanoic acid (10-p-NCA) than F87A(LARV). In addition, they proved capable of hydroxylating ω-(p-nitrophenoxy)octanoic acid (8-p-NCA) which the wild-type enzyme is unable to do. Both variants catalyzed hydroxylation of capric acid, which is not a substrate for the wild-type, with a conversion rate of up to 57%. The chain length specificity of the mutants in fatty acid hydroxylation processes shows a good correlation with their activity towards p-NCA pseudosubstrates. The p-NCA assay therefore, allows high-throughput screening of large mutant libraries for the identification of enzyme variants with the desired catalytic activity towards fatty acids as the natural substrates.     

定向进化改造酪氨酸解氨酶提高大肠杆菌合成对香豆酸产量

对香豆酸是一种具有多种药理活性的天然酚类化合物,也是多种天然药用产物生物合成的前体物质,广泛应用于食品、化妆品、医药等领域。通过微生物合成对香豆酸相对于化学合成和植物提取工艺具有节能减排等优势。但是,目前微生物合成对香豆酸产量较低,难以满足大规模工业发酵生产的要求。为了进一步提高对香豆酸产量,对粘红酵母酪氨酸解氨酶(Tyrosineammonia-lyase,TAL)进行定向进化改造,利用高通量筛选方法从随机突变体文库中筛选TAL催化活性提高的突变体。通过初筛和复筛两轮筛选,从大约10 000个突变体中获得1个TAL催化活性提高1倍的突变体。该突变体包含3个氨基酸突变位点,分别为S9Y、A11N、E518A。进一步通过单点氨基酸饱和突变验证,当S9位点突变为Y、I、N和A11位点突变为N、T、Y时,TAL的催化活性提高1倍以上。通过对S9和A11位点3种类型突变进行组合突变验证,S9Y/A11N和S9N/A11Y突变体的TAL催化活力显著高于其他组合。将S9N/A11Y突变体质粒转入酪氨酸高产菌株CP032。通过摇瓶发酵,该菌株在48 h时的对香豆酸产量达到394.2 mg/L,比对照...     

Application of a lipase-immobilized silica monolith bioreactor to the production of fatty acid methyl esters

We developed a highly efficient bioreactor loaded with a lipase-immobilized non-shrinkable silica monolith by adopting a two-step sol–gel method, i.e., preparing a methyltrimethoxysilane (MTMS)-based silica monolith followed by coating of the latter with more hydrophobic alkyl-substituted silicates that entrapped lipase. We applied this type of bioreactor to the production of fatty acid methyl esters through methanolysis of rapeseed oil in n-hexane by Rhizopus oryzae lipase. As the result of screening alkyltrimethoxysilanes mixed with tetramethoxysilane (TMOS) during sol–gel coating, propyltrimethoxysilane (PTMS) gave the best performance, and the lipase immobilized therein exhibited ca. 10 times higher activity than non-immobilized lipase powder. The amount of the PTMS-based silicates with which the MTMS-based silica monolith was coated was optimized by adjusting the molar ratio of silanes (mixture of PTMS and TMOS at 4:1) to 100 mol of water. Conversion rate was highest at the molar ratio of 0.4 mol silanes to 100 mol of water, which was ca. 10 times higher than that with lipase deposited on the MTMS-based silica monolith. Conversion rate was approximately 1.5 times higher in the flow-through monolith bioreactor than in the batch slurry reactor.     

Comparative effects of perilla and fish oils on the activity and gene expression of fatty acid oxidation enzymes in rat liver

The activity and mRNA level of hepatic enzymes in fatty acid oxidation and synthesis were compared in rats fed diets containing either 15% saturated fat (palm oil), safflower oil rich in linoleic acid, perilla oil rich in α-linolenic acid or fish oil rich in eicosapentaenoic (EPA) and docosahexaenoic acids (DHA) for 15 days. The mitochondrial fatty acid oxidation rate was 50% higher in rats fed perilla and fish oils than in the other groups. Perilla and fish oils compared to palm and safflower oils approximately doubled and more than tripled, respectively, peroxisomal fatty acid oxidation rate. Compared to palm and safflower oil, both perilla and fish oils caused a 50% increase in carnitine palmitoyltransferase I activity. Dietary fats rich in n-3 fatty acids also increased the activity of other fatty acid oxidation enzymes except for 3-hydroxyacyl-CoA dehydrogenase. The extent of the increase was greater with fish oil than with perilla oil. Interestingly, both perilla and fish oils decreased the activity of 3-hydroxyacyl-CoA dehydrogenase measured using short- and medium-chain substrates. Compared to palm and safflower oils, perilla and fish oils increased the mRNA level of many mitochondrial and peroxisomal enzymes. Increases were generally greater with fish oil than with perilla oil. Fatty acid synthase, glucose-6-phosphate dehydrogenase, and pyruvate kinase activity and mRNA level were higher in rats fed palm oil than in the other groups. Among rats fed polyunsaturated fats, activities and mRNA levels of these enzymes were lower in rats fed fish oil than in the animals fed perilla and safflower oils. The values were comparable between the latter two groups. Safflower and fish oils but not perilla oil, compared to palm oil, also decreased malic enzyme activity and mRNA level. Examination of the fatty acid composition of hepatic phospholipid indicated that dietary α-linolenic acid is effectively desaturated and elongated to form EPA and DHA. Dietary perilla oil and fish oil therefore exert similar physiological activity in modulating hepatic fatty acid oxidation, but these dietary fats considerably differ in affecting fatty acid synthesis.     

Glucose stimulates a decrease of the fatty acid saturation degree in Acinetobacter calcoaceticus

The fatty acid composition of Acinetobacter calcoaceticus 69-V was determined under various growth conditions. Saturated, unsaturated, and hydroxy fatty acids with chain lengths of 12–18 carbon atoms predominated in the fatty acid profile. With acetate or propanol as growth substrates, the ratio of saturated to unsaturated fatty acids varied with changes in the temperature. This was the only adaptive mechanism detected that compensated for the physical effects of temperature alterations on the cell membranes. The fatty acid composition of A. calcoaceticus grown at 40 °C had a saturation degree of approximately 50%; after growth at 20 °C it was approximately 35%. In the presence of a carbon and energy source, A. calcoaceticus was able to respond to temperature reductions under oxic conditions regardless of whether fatty acid biosynthesis was inhibited or not. This suggests an aerobic mechanism of fatty acid biosynthesis and the involvement of a fatty acid desaturase system. Addition of the non-growth substrate, glucose, helped the organism to adapt to lower temperature. The molecular mechanism of the aid is not really understood. The oxidation of glucose could provide the desaturase either with electrons directly via a pyrrolo-quinoline-quinone-linked glucose dehydrogenase or with NADH after fatty acid degradation has been initiated by ATP generated by the oxidation of glucose. Received: 19 June 1998 / Accepted: 28 December 1998     

Dehydroepiandrosterone-sulphate replacement improves the human plasma fatty acid profile in plasma of obese women

DHEA-S treatment is used as an anti-aging and anti-obesity hormone therapy in adults; however, it mechanisms of action are not clearly elucidated.The objective of the present work was to analyze the effect of a replacement therapy, which included a daily single oral dose of DHEA-S for three months, on the composition of human plasma fatty acids (FAs) in obese women.In the first study, a randomized, double-blind, placebo-controlled trial was conducted involving 61 postmenopausal women, who were assigned to receive 100 mg/day of DHEA-S (n = 41) or placebo (n = 20) orally for 3 months. In a second study, the effect of DHEA-S treatment on postmenopausal obese women (n = 41) was compared to that in premenopausal obese women (n = 20). Blood samples were collected at the beginning and at the end of the treatment. Plasma FAs were analyzed by gas chromatography.DHEA-S treatment produced significant changes in plasma FAs of both post- and premenopausal women with a reduction of total saturated FAs (SFA) as well as an increase in n − 6 polyunsaturated FA (PUFA). Particularly, in premenopausal women the DHEA-S treatment also increased the plasma n − 3 PUFA percentage. Regarding estimation of desaturase activity, our data showed that Δ6-desaturase was significantly decreased in postmenopausal women after DHEA-S treatment, whereas Δ5-desaturase was increased in the premenopausal group.In conclusion, DHEA-S treatment in obese women modifies plasma FA composition towards a potentially better metabolic profile, mainly by decreasing SFA and increasing n − 6 PUFA in both postmenopausal and premenopausal women.