谷氨酸棒杆菌生产异亮氨酸辅因子策略及其基因组整合研究进展

L?异亮氨酸属于三大支链氨基酸,是人体8种必需氨基酸之一,广泛应用于食品、药品、保健品、化妆品等领域。目前,微生物发酵法是工业生产L?异亮氨酸的主要方法,其中谷氨酸棒杆菌（Corynebacterium glutamicum）是发酵生产L?异亮氨酸的优势菌株,然而随机诱变会使产量的提高能力达到饱和,难以得到更加高产的菌株,因此针对诱变菌株进行理性改造已成为进一步提高产量的主要方式;且随着遗传操作技术在谷氨酸棒杆菌中的应用与优化,代谢工程育种已逐渐取代传统的诱变育种。综述了谷氨酸棒杆菌中L?异亮氨酸的生物合成途径、代谢调控机制和理性改造L?异亮氨酸生产菌株的策略,并对辅助因子工程应用于理性改造及对谷氨酸棒杆菌基因组整合策略进行了系统阐述,以期为工业水平稳定生产L?异亮氨酸高产菌株的基因组整合策略提供参考依据。     

谷氨酸棒杆菌的代谢工程使能技术研究进展

谷氨酸棒杆菌Corynebacterium glutamicum是重要的工业微生物,尤其是在氨基酸工业中,每年用于600余万t氨基酸的生物制造。近年来,谷氨酸棒杆菌代谢工程使能技术正在不断完善,不仅加快了细胞工厂的创建和优化,拓展了底物谱和产物谱,也推动了谷氨酸棒杆菌的基础研究,使谷氨酸棒杆菌成为代谢工程的理想底盘细胞。文中综述了近期针对谷氨酸棒杆菌开发的代谢工程使能技术,着重介绍了基于CRISPR的基因组编辑、基因表达调控、适应性进化和生物传感器等技术的开发和应用。     

合成生物学与代谢工程在谷氨酸棒杆菌产氨基酸中的应用

氨基酸是重要的化合物,在食品、医药、化工等领域具有广泛用途.多种氨基酸可以通过蛋白质水解提取法、化学合成法以及微生物法生产,现如今大部分的氨基酸都开始尝试微生物发酵法实现工业生产.谷氨酸棒杆菌(Corynebacterium glutamicum)作为发酵生产氨基酸的先驱者,其生产的氨基酸产量已达年产数百万吨.随着合成生物学技术以及新一代基因编辑技术的兴起,谷氨酸棒杆菌能生产的氨基酸种类从传统的几种氨基酸扩大到了几乎所有氨基酸及其衍生物.本文综述了近年来利用代谢工程及合成生物学工具对谷氨酸棒杆菌的改造技术,并介绍了一些利用谷氨酸棒杆菌生产传统氨基酸以及非天然氨基酸的典型案例,为谷氨酸棒杆菌突破所有氨基酸生产瓶颈提供参考.     

谷氨酸棒杆菌耐受胁迫机制及工业鲁棒性合成生物学研究进展

谷氨酸棒杆菌Corynebacterium glutamicum作为一般被认为具有生物安全性的一种模式工业微生物,不仅在发酵工业中成功用于大规模生产氨基酸,而且具有合成多种新型化学品的潜力。谷氨酸棒杆菌菌株在生产化合物时,经常会受到各种逆境条件的胁迫,从而降低细胞活力和生产性能。合成生物学的发展为提高谷氨酸棒杆菌的鲁棒性提供了新的技术手段。本文总结了谷氨酸棒杆菌应对发酵过程中各种胁迫的耐受机制。同时,重点介绍提高谷氨酸棒杆菌底盘细胞鲁棒性和耐受性的合成生物学新策略,包括挖掘新的抗逆元件、改造转录调控因子、利用适应性进化策略挖掘抗逆功能模块等。最后,从生物传感器、转录调控因子的筛选和设计、多种调控元件利用等方面对提高谷氨酸棒杆菌底盘细胞鲁棒性进行了展望。     

溶氧量与谷氨酸棒杆菌代谢

正自从1957年Kinoshita等首次描述谷氨酸棒杆菌(Corynebacterium glutamicum)为谷氨酸产生菌[1]以来,其已成为用于氨基酸生产的主要菌株。目前,全世界每年利用谷氨酸棒杆菌生产约100万t L-谷氨酸用于食品调味剂和约45万t L-赖氨酸用作食品添加剂[2]。通过谷氨酸棒状杆菌发酵获得谷氨酸的发酵水平已较高,通过进一步优化工艺来提高产量具有较大困难[3]。     

谷氨酸棒杆菌基因编辑的研究进展

谷氨酸棒杆菌是生产氨基酸、有机酸等的重要菌株,广泛应用于食品、医药领域。利用基因编辑技术对谷氨酸棒杆菌进行基因功能研究,在提高目的产物产量、发现新的基因功能等方面有重要意义。近年来,基因编辑技术发展日新月异,从基于同源重组的传统基因编辑技术到以人工核酸酶介导的基因编辑均在谷氨酸棒杆菌中得到合理应用。其中,CRISPR技术以其快速、简便、编辑效率高等优点成为现阶段研究者用于改造谷氨酸棒杆菌的主要技术,但是更为简单、高效的编辑手段依旧需要进一步研究开发,以获得优良菌株应用于工业生产中。     

代谢工程改造微生物高产氨基酸的策略

氨基酸作为一类营养物质在维持机体正常的生理生化反应方面具有重要的功能,常用作食品、药品和化妆品等的添加剂。氨基酸的生产主要依靠微生物发酵,产氨基酸菌的选育却是制约大规模工业生产氨基酸的重要因素。随着微生物分子育种技术的发展和运用,利用代谢工程改造细胞本身固有的代谢网络,指导氨基酸高产菌的选育已成为当前研究的热点。以谷氨酸棒杆菌(Corynebacterium glutamicum)为例,就该菌株代谢网络的特征以及高产氨基酸的代谢工程策略和应用进行综述。     

基于时间序列转录组筛选谷氨酸棒杆菌内源高效组成型启动子

启动子是重要的转录调控元件,广泛用于工业菌株的代谢工程改造。谷氨酸棒杆菌Corynebacterium glutamicum是重要的氨基酸生产菌株,但已报道的组成型强启动子较少。对谷氨酸高产菌Corynebacterium glutamicum SL4发酵过程的10个时间点样品进行转录组测序,筛选在发酵过程中稳定转录并且转录水平最高的10个基因;分别克隆其启动子序列至红色荧光蛋白(RFP)报告系统,通过荧光强度表征启动子在SL4菌株中的强度,再在野生型C. glutamicum ATCC 13869和ATCC 13032中验证部分启动子的通用性;并采用LacZ蛋白进一步评价强启动子的表达效果。结果显示,成功筛选到3个可以通用的组成型启动子P_(cysK)、P_(gapA)和P_(fumC)。其中P_(cysK)的表达强度最高,与诱导型强启动子P_(tac)对比,在SL4和13869菌株中均达到其2倍(RFP)和4倍(LacZ)以上;在ATCC 13032菌株中,P_(cysK)的表达强度为P_(tac)的0.3-0.4倍。Pcys K首次被报道为强启动子,可用于谷氨酸棒杆菌强化合成途径的代谢工程改造。     

谷氨酸棒杆菌H+-ATPase基因失活提高谷氨酸产生量

为了证实在谷氨酸棒杆菌中,利用H⁺-ATPase基因失活构建高产谷氨酸基因工程菌的应用可行性,通过重组PCR技术部分缺失H⁺-ATPaseγ亚基基因序列,采用插入失活方法构建H⁺-ATPase失活的谷氨酸棒杆菌。考察了其谷氨酸产生能力及对生长速率的影响。实验结果表明,H⁺-ATPase失活的谷氨酸棒杆菌在含有100g/L的葡萄糖培养基中摇瓶发酵,其谷氨酸最大累积量为51.6g/L, 比野生菌株提高了42.9%。生长速率研究结果表明,H⁺-ATPase失活的谷氨酸棒杆菌生长速率略低于野生谷氨酸棒杆菌。证实了H⁺-ATPase基因失活对提高谷氨酸产量的作用,为利用H⁺-ATPase基因构建高产谷氨酸基因工程菌株提供了科学依据。     

TCA循环关键节点对L-谷氨酸合成的影响

谷氨酸是一种重要的氨基酸,其衍生出来的高值化产品具有广泛的应用,市场需求量巨大。文中通过对出发菌株谷氨酸棒杆菌Corynebacterium glutamicum E01和谷氨酸高产菌C. glutamicum G01进行转录组测序与重测序分析,挑选中心代谢途径中转录水平和基因水平上存在差异的基因进行研究,以挖掘出对谷氨酸合成影响较大的基因进一步提高谷氨酸的产量。草酰乙酸节点和α-酮戊二酸节点在谷氨酸合成中扮演着重要角色,探索研究了草酰乙酸节点和α-酮戊二酸节点对谷氨酸生产的扰动影响。综合以上实验结果构建的整合菌株,5 L发酵罐发酵过程中其菌体生长速率较原始菌略有降低,但48h的谷氨酸产量高达(136.09±5.53)g/L,较原始菌的(93.53±4.52)g/L提高了45.5%;糖酸转化率提高至58.9%,较原始菌的45.2%提高了13.7%。可见,上述实验策略的应用在一定程度上提高了谷氨酸产量和糖酸转化率,为谷氨酸棒杆菌的代谢工程改造提供了理论基础。     

Metabolic phenotype of phosphoglucose isomerase mutants of Corynebacterium glutamicum

A series of experiments reported in the literature using fluxomics as an efficient functional genomics tool revealed that the L-lysine production of the Corynebacterium glutamicum strain MH20-22B correlates with the extent of intracellular NADPH supply. Some alternative metabolic engineering strategies to increase intracellular NADPH supply in the C. glutamicum strain DSM5715 were considered and finally the redirection of carbon flux through the pentose phosphate pathway with two NADPH generating enzymatic reactions was favored. Elsewhere, the construction of a phosphoglucose isomerase (Pgi) null mutant of the C. glutamicum strain DSM5715 has been described by utilizing genetic engineering as well as some aspects of its metabolic phenotype. Most interestingly, it was shown that not only could the L-lysine formation be increased by 1.7-fold but the by-product concentration for the null mutant strain was also able to be drastically reduced. In this publication we discuss this metabolic phenotype in detail and present additional data on by-product formation as well as yield considerations. Results from isotope based metabolic flux analysis in combination with considerations on NADPH metabolism clearly exclude the existence of Pgi isoenzymes in C. glutamicum strain DSM5715. The genome region containing the pgi gene was analyzed. It cannot be excluded that polar effects might have been caused by the disruption of the pgi gene and might have contributed to the observed metabolic phenotype of C. glutamicum Pgi mutants. We illustrate growth characteristics of a Pgi mutant of an industrial L-lysine production strain. A reduced growth rate and a biphasic growth behavior was observed. The importance of NADPH reoxidation for well balanced growth in Pgi mutants is discussed. Another phosphoglucose isomerase mutant of C. glutamicum has been described in literature with which an increase in L-lysine yield from 42 to 52% was observed. This finding highlights the general potential of metabolic flux redirection towards the pentose phosphate pathway, which could be used for metabolic engineering of the biotechnological synthesis of (1) aromatic amino acids and (2) chemicals whose synthesis depends on intracellular NADPH supply.     

谷氨酸棒杆菌中氨基酸分泌转运蛋白及其代谢改造研究进展

氨基酸是一类在食品、医药及化工等领域具有广泛应用的重要化合物。谷氨酸棒杆菌Corynebacterium glutamicum是生物合成氨基酸最重要的微生物菌株,其年产各类氨基酸超过百万吨。谷氨酸棒杆菌高产氨基酸除具有强大的合成代谢能力外,高效的分泌转运能力也是不可忽略的分子基础。文中综述了近年来谷氨酸棒杆菌中氨基酸分泌转运蛋白及其代谢改造的研究进展,并展望了未来发展方向,为进一步改造提升其发酵生产氨基酸的能力提供了可资借鉴的资料。     

谷氨酸棒状杆菌厌氧产丁二酸的发酵条件

考察谷氨酸棒状杆菌ATCC13032Δldh厌氧产丁二酸的发酵条件。结果发现:补加NaHCO3的效果最好,并且考察了NaHCO3浓度对葡萄糖转化速率及丁二酸生成速率的影响。运用代谢流分析方法分析了乳酸脱氢酶基因敲除对谷氨酸棒状杆菌厌氧代谢的影响,发现乳酸脱氢酶基因敲除导致磷酸烯醇式丙酮酸生成丁二酸的流量提高了214.3%,流向乳酸的流量变为0;分批厌氧转化36 h生成41.2 g/L丁二酸,产率45.0%。     

From genome sequence to integrated bioprocess for succinic acid production by <Emphasis Type="Italic">Mannheimia succiniciproducens</Emphasis>

Mannheimia succiniciproducens is a capnophilic gram-negative bacterium isolated from bovine rumen. Wild-type M. succiniciproducens can produce succinic acid as a major fermentation product with acetic, formic, and lactic acids as byproducts during the anaerobic cultivation using several different carbon sources. Succinic acid is an important C4 building block chemical for many applications. Here, we review the progress made with M. succiniciproducens for efficient succinic acid production; the approaches taken towards the development of an integrated process for succinic acid production are described, which include strain isolation and characterization, complete genome sequencing and annotation, development of genetic tools for metabolic engineering, strain development by systems approach of integrating omics and in silico metabolic analysis, and development of fermentation and recovery processes. We also describe our current effort on further improving the performance of M. succiniciproducens and optimizing the mid- and downstream processes. Finally, we finish this mini-review by discussing the issues that need to be addressed to make this process of fermentative succinic acid production employing M. succiniciproducens to reach the industrial-scale process.     

Engineering of unconventional yeast Yarrowia lipolytica for efficient succinic acid production from glycerol at low pH

Yarrowia lipolytica is considered as a potential candidate for succinic acid production because of its innate ability to accumulate citric acid cycle intermediates and its tolerance to acidic pH. Previously, a succinate-production strain was obtained through the deletion of succinate dehydrogenase subunit encoding gene Ylsdh5. However, the accumulation of by-product acetate limited further improvement of succinate production. Meanwhile, additional pH adjustment procedure increased the downstream cost in industrial application. In this study, we identified for the first time that acetic acid overflow is caused by CoA-transfer reaction from acetyl-CoA to succinate in mitochondria rather than pyruvate decarboxylation reaction in SDH negative Y. lipolytica. The deletion of CoA-transferase gene Ylach eliminated acetic acid formation and improved succinic acid production and the cell growth. We then analyzed the effect of overexpressing the key enzymes of oxidative TCA, reductive carboxylation and glyoxylate bypass on succinic acid yield and by-products formation. The best strain with phosphoenolpyruvate carboxykinase (ScPCK) from Saccharomyces cerevisiae and endogenous succinyl-CoA synthase beta subunit (YlSCS2) overexpression improved succinic acid titer by 4.3-fold. In fed-batch fermentation, this strain produced 110.7 g/L succinic acid with a yield of 0.53 g/g glycerol without pH control. This is the highest succinic acid titer achieved at low pH by yeast reported worldwide, to date, using defined media. This study not only revealed the mechanism of acetic acid overflow in SDH negative Y. lipolytica, but it also reported the development of an efficient succinic acid production strain with great industrial prospects.     

Genome-scale analysis of Mannheimia succiniciproducens metabolism

Mannheimia succiniciproducens MBEL55E isolated from bovine rumen is a capnophilic gram-negative bacterium that efficiently produces succinic acid, an industrially important four carbon dicarboxylic acid. In order to design a metabolically engineered strain which is capable of producing succinic acid with high yield and productivity, it is essential to optimize the whole metabolism at the systems level. Consequently, in silico modeling and simulation of the genome-scale metabolic network was employed for genome-scale analysis and efficient design of metabolic engineering experiments. The genome-scale metabolic network of M. succiniciproducens consisting of 686 reactions and 519 metabolites was constructed based on reannotation and validation experiments. With the reconstructed model, the network structure and key metabolic characteristics allowing highly efficient production of succinic acid were deciphered; these include strong PEP carboxylation, branched TCA cycle, relative weak pyruvate formation, the lack of glyoxylate shunt, and non-PTS for glucose uptake. Constraints-based flux analyses were then carried out under various environmental and genetic conditions to validate the genome-scale metabolic model and to decipher the altered metabolic characteristics. Predictions based on constraints-based flux analysis were mostly in excellent agreement with the experimental data. In silico knockout studies allowed prediction of new metabolic engineering strategies for the enhanced production of succinic acid. This genome-scale in silico model can serve as a platform for the systematic prediction of physiological responses of M. succiniciproducens to various environmental and genetic perturbations and consequently for designing rational strategies for strain improvement.     

Model-aided atpE gene knockout strategy in Escherichia coli for enhanced succinic acid production from glycerol

Succinic acid is an important platform chemical with a variety of applications. Model-guided metabolic engineering strategies in Escherichia coli for strain improvement to increase succinic acid production using glucose and glycerol remain largely unexplored. Herein, we report what are, to our knowledge, the first metabolic knockout of the atpE gene to have increased succinic acid production using both glucose and alternative glycerol carbon sources in E. coli. Guided by a genome-scale metabolic model, we engineered the E. coli host to enhance anaerobic production of succinic acid by deleting the atpE gene, thereby generating additional reducing equivalents by blocking H⁺ conduction across the mutant cell membrane. This strategy produced 1.58 and .49 g l^?1 of succinic acid from glycerol and glucose substrate, respectively. This work further elucidates a model-guided and/or system-based metabolic engineering, involving only a single-gene deletion strategy for enhanced succinic acid production in E. coli.     

Metabolic engineering of Corynebacterium glutamicum for production of 1,5-diaminopentane from hemicellulose

In the present work, the bio-based production of 1,5-diaminopentane (cadaverine), an important building block for bio-polyamides, was extended to hemicellulose a non-food raw material. For this purpose, the metabolism of 1,5-diaminopentane-producing Corynebacterium glutamicum was engineered to the use of the C(5) sugar xylose. This was realized by heterologous expression of the xylA and xylB genes from Escherichia coli, mediating the conversion of xylose into xylulose 5-phosphate (an intermediate of the pentose phosphate pathway), in a defined diaminopentane-producing C. glutamicum strain, recently obtained by systems metabolic engineering. The created mutant, C. glutamicum DAP-Xyl1, exhibited efficient production of the diamine from xylose and from mixtures of xylose and glucose. Subsequently, the novel strain was tested on industrially relevant hemicellulose fractions, mainly containing xylose and glucose as carbon source. A two-step process was developed, comprising (i) enzymatic hydrolysis of hemicellulose from dried oat spelts, and (ii) biotechnological 1,5-diaminopentane production from the obtained hydrolysates with the novel C. glutamicum strain. This now opens a future avenue towards bio-based 1,5-diaminopentane and bio-polyamides thereof from non-food raw materials.     

Increasing available NADH supply during succinic acid production by Corynebacterium glutamicum

A critical factor in the biotechnological production of succinic acid with Corynebacterium glutamicum is the sufficient supply of NADH. It is conceivable that cofactor availability and the proportion of cofactor in the active form may play an important role in dictating the succinic acid yield. PntAB genes from Escherichia coli can directly catalyze the reversible hydride transfer and adjust the dynamic balance between NADP(H) and NAD(H). Hence, we studied the physiological effect of coenzyme systems by expressing the membrane‐bound transhydrogenase pntAB genes. We have shown experimentally that the pntAB genes could function as an alternative source of NADH. In an anaerobic fermentation with C. glutamicum NC‐3‐pntAB, a 16% higher succinic acid yield and a 57% higher production from glucose were obtained by pntAB expression. Moreover, the formation of by‐products was significantly decreased. The concomitant increase in the consumption of intracellular NADPH from 0.6 to 1.2 mmol/g CDW and the increased NADH/NAD⁺ ratio resulted from introduction of pntAB, suggesting that the membrane‐bound transhydrogenase converted excess NADPH to NADH for succinic acid production. Finally, we explored whether the transhydrogenase had different effects on the succinic acid formation on different carbon sources. The succinic acid yield was increased in the presence of pntAB by 16% on glucose, 7% on sucrose, and without large influence on fructose and xylose. The results of this study demonstrated that the effectiveness of cofactor manipulation could be a promising strategy applied in metabolic engineering. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:12–19, 2015     

调控大肠杆菌胞内ATP和NADH水平促进琥珀酸生产

琥珀酸作为一种重要的C4平台化合物,广泛应用于食品、化学、医药等领域。利用大肠杆菌(Escherichia coli)发酵生产琥珀酸受胞内辅因子不平衡的影响,存在产率低、生产强度低、副产物多等问题。为此,对不同氧气条件下琥珀酸产量和化学计量学分析发现,微厌氧条件下E.coli FMME-N-26高效积累琥珀酸需要借助三羧酸循环(tricarboxylic acid cycle,TCA)为还原性三羧酸途径(reductive tricarboxylic acid pathway,r-TCA)提供足够的ATP和NADH。通过减少ATP消耗、强化ATP合成、阻断NADH竞争途径和构建NADH回补路径等代谢工程策略,组合调控胞内ATP与NADH含量,获得工程菌株E.coli FW-17。通过发酵条件优化,菌株E.coli FW-17在5 L发酵罐能积累139.52 g/L琥珀酸,比出发菌株提高了17.81%,乙酸浓度为1.40 g/L,降低了67.59%。进一步在1000 L发酵罐中进行放大实验,琥珀酸产量和乙酸浓度分别为140.2 g/L和1.38 g/L。