Gene Regulatory and Metabolic Adaptation Processes of Dinoroseobacter shibae DFL12T during Oxygen Depletion
Gene Regulatory and Metabolic Adaptation Processes of Dinoroseobacter shibae DFL12T during Oxygen Depletion
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DOI：
10.1074/jbc.m113.545004
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发表时间：
2014-05-09
影响因子：
4.8
通讯作者：
Schomburg, Dietmar
中科院分区：
文献类型：
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作者：
Laass, Sebastian;Kleist, Sarah;Schomburg, Dietmar
背景：细菌Dinoroseasticshietum暴露于环境缺氧。结果：系统生物学分析显示了D.缺氧时会出现休克结论：缺氧导致代谢危机，由于缺乏再生的ATP和还原当量，直到反硝化建立。重要性：本文阐述了海洋细菌对缺氧呼吸的适应过程，代谢的灵活性是海洋玫瑰枝细菌生态成功的关键。我们通过代谢组学、蛋白质组学和转录组学分析相结合的方法研究了甲藻DFL 12（T）对缺氧生活的代谢适应和基因表达的潜在变化。在恒化器中使用硝酸盐作为末端电子受体进行连续缺氧期间的时间分辨研究。反硝化机制的形成在转录和蛋白质组水平上被发现增强，表明D。shiodine DFL 12（T）建立了硝酸盐呼吸以补偿电子受体氧的消耗。同时，诱导精氨酸发酵。在过渡状态期间，发现生长和ATP浓度降低，如A（578）值和活细胞计数降低所反映的。与此同时，发现中央代谢（包括代谢产物生成、蛋白质生物合成和嘌呤/嘧啶合成）短暂减少，与细胞构建模块需求的减少一致。令人惊讶的是，在缺氧条件下长时间孵育期间观察到聚-3-羟基丁酸酯的积累。一种可能的解释是在聚-3-羟基丁酸合成（NADPH汇）过程中积累的代谢物的储存和NADP（+）从NADPH的再生。虽然D. shiphilis DFL 12（T）在黑暗中培养，细菌叶绿素的生物合成增加，可能为通过有氧无氧磷酸化产生额外的能量做准备。总体而言，缺氧导致代谢危机，部分阻断途径和代谢物积累。作为回应，主要的能源消耗过程被减少，直到替代呼吸脱氮机制开始运作。
Background: The bacterium Dinoroseobacter shibae was exposed to environmental anoxia. Results: Systems biology analyses showed the time-resolved cellular adaptation processes of D. shibae during oxygen depletion. Conclusion: Oxygen depletion led to a metabolic crisis due to the missing regeneration of ATP and reduction equivalents, until denitrification was established. Significance: Here we have elucidated the adaptation processes of marine bacteria to anoxic respiration.Metabolic flexibility is the key to the ecological success of the marine Roseobacter clade bacteria. We investigated the metabolic adaptation and the underlying changes in gene expression of Dinoroseobacter shibae DFL12(T) to anoxic life by a combination of metabolome, proteome, and transcriptome analyses. Time-resolved studies during continuous oxygen depletion were performed in a chemostat using nitrate as the terminal electron acceptor. Formation of the denitrification machinery was found enhanced on the transcriptional and proteome level, indicating that D. shibae DFL12(T) established nitrate respiration to compensate for the depletion of the electron acceptor oxygen. In parallel, arginine fermentation was induced. During the transition state, growth and ATP concentration were found to be reduced, as reflected by a decrease of A(578) values and viable cell counts. In parallel, the central metabolism, including gluconeogenesis, protein biosynthesis, and purine/pyrimidine synthesis was found transiently reduced in agreement with the decreased demand for cellular building blocks. Surprisingly, an accumulation of poly-3-hydroxybutanoate was observed during prolonged incubation under anoxic conditions. One possible explanation is the storage of accumulated metabolites and the regeneration of NADP(+) from NADPH during poly-3-hydroxybutanoate synthesis (NADPH sink). Although D. shibae DFL12(T) was cultivated in the dark, biosynthesis of bacteriochlorophyll was increased, possibly to prepare for additional energy generation via aerobic anoxygenic photophosphorylation. Overall, oxygen depletion led to a metabolic crisis with partly blocked pathways and the accumulation of metabolites. In response, major energy-consuming processes were reduced until the alternative respiratory denitrification machinery was operative.