基于基因组分析的VC发酵混菌体系共生机制及功能强化
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摘要
剖析Ketogulonigenium vulgare及其伴生菌Bacillus sp.相互作用机制并对混菌体系进行调控，及构建高产维生素C前体的菌株，是优化维生素C工业生产的两个重要方面。本文对该混菌体系中的产酸菌株和伴生菌株进行基因组水平系统分析，探究两菌形成共生关系的遗传背景和代谢互作机制；构建产古龙酸途径及其辅因子吡咯喹啉醌（PQQ）合成的功能模块，通过功能模块之间最优组合及其与底盘细胞之间的适应性进化，强化混菌体系的发酵水平。
采用高通量测序技术获得实验室产酸菌K. vulgare HB602全基因组序列和工业伴生菌Bacillus endophyticus Hbe603的基因组框架序列。通过基因组分析，K.vulgare的共生特性有赖于编码了分解、吸收并利用伴生菌提供的蛋白类、肽类和氨基酸类物质的强大系统，响应环境变化的转录调控蛋白及趋化调控系统。其高效的山梨糖转化能力与基因组中5拷贝的山梨糖脱氢酶基因和2拷贝的山梨酮脱氢酶基因相关。伴生菌基因组编码完整的芽孢形成途径，但缺失大量芽孢衣合成基因及rap-phr信号系统，具有独特的芽孢衣外层结构和起始芽孢形成的调控机制，与其作为优良伴生菌的特性相关。利用K. vulgare及伴生菌B. megaterium的全基因组数据构建基因组水平代谢网络，发现产酸菌在碳水化合物、脂和辅因子/维生素代谢途径中所包含代谢反应的比例低于伴生菌，是其生长缓慢的主要原因；伴生菌可能通过弥补其在半乳糖代谢、丁酸代谢、脂肪酸分解、谷氨酸合成、甲硫氨酸循环、缬氨酸/亮氨酸/异亮氨酸降解、尿素循环、色氨酸代谢、辅因子/维生素合成等途径中的代谢缺陷形成代谢互补关系，构成稳定的共生体系。
对混菌体系产古龙酸途径进行功能强化，构建三种产酸能力不同的产酸模块和三种产PQQ水平不同的辅因子合成模块，将两类模块进行搭配组合获得九种组合模块，并发现在K. vulgare HB602中最适配的组合形式ss-pqqABCDEN，可提高混菌体系产古龙酸水平20%（79.1±0.6g/L）。通过在营养条件下50次混菌转接传代的适应性进化，强化了组合模块在工业菌株K. vulgare HKv604中的功能，其中sdh-pqqABCDEN模块和ss-pqqABCDEN模块在工业底盘细胞内发酵水平提高最为显著，混菌产古龙酸浓度达到79.47±0.00g/L和80.48±0.55g/L。
Clarifying the interaction between Ketogulonigenium vulgare and its companionBacillus sp. and obtaining a consortium with enhanced2-keto-L-gulonic acid (2-KLG)production are of great importance to vitamin C industry. In this study, the interactionwithin the consortium was systematically analyzed on genome scale. L-sorboseconversion pathway and cofactor pyrroloquinoline quinone (PQQ) synthesis pathwaywere constructed into a series of modules, and the optimal combination betweenmodules or adaptive evolution within the chassis were investigated to increase theproduction of2-KLG.
Genome sequencing of the laboratory strain K. vulgare HB602and the industrialcompanion strain Bacillus endophyticus Hbe603were performed by next-generationDNA sequencing technologies. The K. vulgare genome encoded a large number ofproteins involved in degrading, assimilating and metabolizing proteins, peptides oramino acids, which might be provided by the companion. Various transcriptionalregulators, chemotaxis regulators and the flagella synthesis system were predicted tobe associated with cellular response.5copies of sorbose dehydrogenase and2copiesof sorbosone dehydrogenase were present in the genome, and multi-copy of these keyenzymes in the L-sorbose pathway was responsible for efficient substrate conversion.The B. endophyticus genome contained a set of genes involved in spore formation,while lacked several spore coat synthesis genes and the rap-phr system coding genes.It indicated that B. endophyticus was able to form spore with specific spore coatstructure, which was initiated by a certain regulation mechanism. Comparisonbetween the genome scale metabolic networks of K. vulgare and companion B.megaterium showed that K. vulgare contained less reactions in metabolism ofcarbohydrate, lipid, cofactors and vitamins, indicating the poor growth of K. vulgare.The companion bacterium was necessary for K. vulgare to complement its metabolicdefect in galactose and butanoate metabolism, lipid degradation, glutamate synthesis,methionine cycle, valine/leucine/isoleucine degradation, urea cycle, tryptophanmetabolism and metabolism of cofactors and vitamins.
Sorbose/sorbosone dehydrogenase genes (sdh and sndh) and synthesis genes(pqqABCDEN) of the adjoint cofactor PQQ was constructed into3L-sorbose conversion modules and3PQQ synthesis modules respectively.9combinations ofthese two types of modules were constructed to investigate the adaptation betweenmodules, and the combinational module of ss-pqqABCDEN exhibited optimaladaptation by a20%increase in the production of2-KLG (79.1±0.6g/L) than that ofthe parental K. vulgare HB602(65.9±0.4g/L) in co-cultures. The enhancement of2-KLG production in engineered industrial strain K. vulgare HKv604was achieved byco-cultured adaptive evolution of50transfers. Combinational modules ofsdh-pqqABCDEN and ss-pqqABCDEN demonstrated improved adaptation to theindustrial chassis consortium, which produced higher concentration of2-KLG(79.47±0.00g/L and80.48±0.55g/L) than they performed before adaptation.
采用高通量测序技术获得实验室产酸菌K. vulgare HB602全基因组序列和工业伴生菌Bacillus endophyticus Hbe603的基因组框架序列。通过基因组分析，K.vulgare的共生特性有赖于编码了分解、吸收并利用伴生菌提供的蛋白类、肽类和氨基酸类物质的强大系统，响应环境变化的转录调控蛋白及趋化调控系统。其高效的山梨糖转化能力与基因组中5拷贝的山梨糖脱氢酶基因和2拷贝的山梨酮脱氢酶基因相关。伴生菌基因组编码完整的芽孢形成途径，但缺失大量芽孢衣合成基因及rap-phr信号系统，具有独特的芽孢衣外层结构和起始芽孢形成的调控机制，与其作为优良伴生菌的特性相关。利用K. vulgare及伴生菌B. megaterium的全基因组数据构建基因组水平代谢网络，发现产酸菌在碳水化合物、脂和辅因子/维生素代谢途径中所包含代谢反应的比例低于伴生菌，是其生长缓慢的主要原因；伴生菌可能通过弥补其在半乳糖代谢、丁酸代谢、脂肪酸分解、谷氨酸合成、甲硫氨酸循环、缬氨酸/亮氨酸/异亮氨酸降解、尿素循环、色氨酸代谢、辅因子/维生素合成等途径中的代谢缺陷形成代谢互补关系，构成稳定的共生体系。
对混菌体系产古龙酸途径进行功能强化，构建三种产酸能力不同的产酸模块和三种产PQQ水平不同的辅因子合成模块，将两类模块进行搭配组合获得九种组合模块，并发现在K. vulgare HB602中最适配的组合形式ss-pqqABCDEN，可提高混菌体系产古龙酸水平20%（79.1±0.6g/L）。通过在营养条件下50次混菌转接传代的适应性进化，强化了组合模块在工业菌株K. vulgare HKv604中的功能，其中sdh-pqqABCDEN模块和ss-pqqABCDEN模块在工业底盘细胞内发酵水平提高最为显著，混菌产古龙酸浓度达到79.47±0.00g/L和80.48±0.55g/L。
Clarifying the interaction between Ketogulonigenium vulgare and its companionBacillus sp. and obtaining a consortium with enhanced2-keto-L-gulonic acid (2-KLG)production are of great importance to vitamin C industry. In this study, the interactionwithin the consortium was systematically analyzed on genome scale. L-sorboseconversion pathway and cofactor pyrroloquinoline quinone (PQQ) synthesis pathwaywere constructed into a series of modules, and the optimal combination betweenmodules or adaptive evolution within the chassis were investigated to increase theproduction of2-KLG.
Genome sequencing of the laboratory strain K. vulgare HB602and the industrialcompanion strain Bacillus endophyticus Hbe603were performed by next-generationDNA sequencing technologies. The K. vulgare genome encoded a large number ofproteins involved in degrading, assimilating and metabolizing proteins, peptides oramino acids, which might be provided by the companion. Various transcriptionalregulators, chemotaxis regulators and the flagella synthesis system were predicted tobe associated with cellular response.5copies of sorbose dehydrogenase and2copiesof sorbosone dehydrogenase were present in the genome, and multi-copy of these keyenzymes in the L-sorbose pathway was responsible for efficient substrate conversion.The B. endophyticus genome contained a set of genes involved in spore formation,while lacked several spore coat synthesis genes and the rap-phr system coding genes.It indicated that B. endophyticus was able to form spore with specific spore coatstructure, which was initiated by a certain regulation mechanism. Comparisonbetween the genome scale metabolic networks of K. vulgare and companion B.megaterium showed that K. vulgare contained less reactions in metabolism ofcarbohydrate, lipid, cofactors and vitamins, indicating the poor growth of K. vulgare.The companion bacterium was necessary for K. vulgare to complement its metabolicdefect in galactose and butanoate metabolism, lipid degradation, glutamate synthesis,methionine cycle, valine/leucine/isoleucine degradation, urea cycle, tryptophanmetabolism and metabolism of cofactors and vitamins.
Sorbose/sorbosone dehydrogenase genes (sdh and sndh) and synthesis genes(pqqABCDEN) of the adjoint cofactor PQQ was constructed into3L-sorbose conversion modules and3PQQ synthesis modules respectively.9combinations ofthese two types of modules were constructed to investigate the adaptation betweenmodules, and the combinational module of ss-pqqABCDEN exhibited optimaladaptation by a20%increase in the production of2-KLG (79.1±0.6g/L) than that ofthe parental K. vulgare HB602(65.9±0.4g/L) in co-cultures. The enhancement of2-KLG production in engineered industrial strain K. vulgare HKv604was achieved byco-cultured adaptive evolution of50transfers. Combinational modules ofsdh-pqqABCDEN and ss-pqqABCDEN demonstrated improved adaptation to theindustrial chassis consortium, which produced higher concentration of2-KLG(79.47±0.00g/L and80.48±0.55g/L) than they performed before adaptation.
引文
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