Genome streamlining is a feasible strategy for constructing an optimum microbial chassis for synthetic biology applications. Genomic islands (GIs) are usually regarded as foreign DNA sequences, which can be obtained by horizontal gene transfer among microorganisms. A model strain Pseudomonas putida KT2440 has broad applications in biocatalysis, biotransformation and biodegradation. In this study, the identified GIs in P. putida KT2440 accounting for 4.12% of the total genome size were deleted to generate a series of genome-reduced strains. The mutant KTU-U13 with the largest deletion was advantageous over the original strain KTU in several physiological characteristics evaluated. The mutant KTU-U13 showed high plasmid transformation efficiency and heterologous protein expression capacity compared with the original strain KTU. The metabolic phenotype analysis showed that the types of carbon sources utilized by the mutant KTU-U13 and the utilization capabilities for certain carbon sources were increased greatly. The polyhydroxyalkanoate (PHA) yield and cell dry weight of the mutant KTU-U13 were improved significantly compared with the original strain KTU. The chromosomal integration efficiencies for the γ-hexachlorocyclohexane (γ-HCH) and 1,2,3-trichloropropane (TCP) biodegradation pathways were improved greatly when using the mutant KTU-U13 as the recipient cell and enhanced degradation of γ-HCH and TCP by the mutant KTU-U13 was also observed. The mutant KTU-U13 was able to stably express a plasmid-borne zeaxanthin biosynthetic pathway, suggesting the excellent genetic stability of the mutant. These desirable traits make the GIs-deleted mutant KTU-U13 an optimum chassis for synthetic biology applications. The present study suggests that the systematic deletion of GIs in bacteria may be a useful approach for generating an optimal chassis for the construction of microbial cell factories.

中文翻译：

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恶臭假单胞菌KT2440基因组中基因组岛的缺失可以为合成生物学应用创造一个最佳的底盘

基因组优化是为合成生物学应用构建最佳微生物底盘的可行策略。基因岛（GIs）通常被视为外源DNA序列，可以通过微生物之间的水平基因转移获得。模型菌株恶臭假单胞菌KT2440在生物催化，生物转化和生物降解中具有广泛的应用。在这项研究中，删除了已鉴定的恶臭假单胞菌KT2440中占总基因组大小4.12％的GI，以生成一系列减少基因组的菌株。在评估的几个生理特征中，具有最大缺失的突变体KTU-U13优于原始菌株KTU。与原始菌株KTU相比，突变体KTU-U13显示出高质粒转化效率和异源蛋白表达能力。代谢表型分析表明，突变体KTU-U13利用的碳源类型和对某些碳源的利用能力大大提高。与原始菌株KTU相比，突变体KTU-U13的聚羟基链烷酸酯（PHA）产量和细胞干重得到显着提高。当使用突变体KTU-U13作为受体细胞时，γ-六氯环己烷（γ-HCH）和1,2,3-三氯丙烷（TCP）生物降解途径的染色体整合效率大大提高，并增强了γ-HCH和TCP的降解还观察到由突变体KTU-U13引起的突变。突变体KTU-U13能够稳定表达质粒携带的玉米黄质生物合成途径，表明该突变体具有出色的遗传稳定性。这些理想的特性使缺失GIs的突变体KTU-U13成为合成生物学应用的最佳底盘。本研究表明，细菌中胃肠道的系统性缺失可能是产生用于构建微生物细胞工厂的最佳底盘的有用方法。