An Integrated Systems Approach Unveils New Aspects of Microoxia-mediated Regulation in Bradyrhizobium diazoefficiens

Using an integrated systems approach, the expressed proteome of B. diazoefficiens strain 110scp4 was measured under i) normal, oxic growth, and ii) microoxic growth condtions. This included, as a first step, the sequencing and de novo assembly of the genome of this widely used rhizobial model strain, which turned out to harbor several deletions and insertions compared to the B. diazoefficiens USDA 110 NCBI reference genome. With this optimal basis in hand, a shotgun proteomics approach relying on a slightly adapated FASP protocol was carried out, allowing to identify 2900 (oxia) and 2826 (microoxia) proteins, respectively, thereby largely expanding the proteome known to be expressed under microoxic conditions.

本研究采用整合系统生物学研究策略，对固氮慢生根瘤菌（Bradyrhizobium diazoefficiens）菌株110scp4的表达蛋白质组，分别在两种生长条件下开展测定：i）正常有氧生长条件，ii）微氧生长条件。本研究的首要步骤为对这一被广泛应用的根瘤菌模式菌株的基因组进行测序与从头组装；经比对发现，该菌株相较于固氮慢生根瘤菌USDA 110的NCBI参考基因组，存在多处缺失与插入变异。在此优化后的基因组基础上，本研究采用稍加改良的过滤辅助样品制备（Filter-Aided Sample Preparation，FASP）方案实施鸟枪蛋白质组学分析，最终分别鉴定出2900个（有氧条件）与2826个（微氧条件）蛋白质，由此大幅拓展了当前已知的微氧条件下表达的蛋白质组覆盖范围。