Abstract：
Microbial instability is a common problem during bio-production based on microbial hosts. Halomonas bluephagenesis has been developed as a chassis for next generation industrial biotechnology (NGIB) under open and unsterile conditions. However, the hidden genomic information and peculiar metabolism have significantly hampered its deep exploitation for cell-factory engineering. Based on the freshly completed genome sequence of H. bluephagenesis TD01, which reveals 1889 biological process-associated genes grouped into 84 GO-slim terms. An enzyme constrained genome-scale metabolic model Halo-ecGEM was constructed, which showed strong ability to simulate fed-batch fermentations. A visible salt-stress responsive landscape was achieved by combining GO-slim term enrichment and CVT-based omics profiling, demonstrating that cells deploy most of the protein resources by force to support the essential activity of translation and protein metabolism when exposed to salt stress. Under the guidance of Halo-ecGEM, eight transposases were deleted, leading to a significantly enhanced stability for its growth and bioproduction of various polyhydroxyalkanoates (PHA) including 3-hydroxybutyrate (3HB) homopolymer PHB, 3HB and 3-hydroxyvalerate (3HV) copolymer PHBV, as well as 3HB and 4-hydroxyvalerate (4HB) copolymer P34HB. This study sheds new light on the metabolic characteristics and stress-response landscape of H. bluephagenesis, achieving for the first time to construct a long-term growth stable chassis for industrial applications. For the first time, it was demonstrated that genome encoded transposons are the reason for microbial instability during growth in flasks and fermentors.
摘要：
微生物不稳定性是基于微生物宿主的生物生产过程中的常见问题。Halomonasbluphagenesis已被开发为在开放和非无菌条件下用于下一代工业生物技术（NGIB）的底盘。然而,隐藏的基因组信息和特殊的新陈代谢极大地阻碍了其对细胞工厂工程的深度开发。基于新完成的H.bluphenesisTD01的基因组序列，该序列揭示了1889个与生物过程相关的基因，分为84个GO-slim项。构建了酶约束的基因组尺度代谢模型Halo-ecGEM，具有很强的模拟补料分批发酵能力。通过结合GO-苗条术语富集和基于CVT的组学分析，实现了可见的盐胁迫响应景观。证明细胞通过武力部署大部分蛋白质资源，以支持在暴露于盐胁迫时的翻译和蛋白质代谢的基本活动。在Halo-ecGEM的指导下，八个转座酶被删除，导致其生长和生物生产的各种聚羟基链烷酸酯（PHA），包括3-羟基丁酸酯（3HB）均聚物PHB的稳定性显着增强，3HB和3-羟基戊酸酯（3HV）共聚物PHBV，以及3HB和4-羟基戊酸酯(4HB)共聚物P34HB。本研究为蓝藻的代谢特征和应激反应景观提供了新的思路，首次实现为工业应用构建长期增长稳定的底盘。第一次,研究表明，基因组编码的转座子是微生物在培养瓶和发酵罐生长过程中不稳定的原因。
