Characterizing the interplay of rubisco 1 and nitrogenase enzymes in anaerobic-photoheterotrophically grown Rhodopseudomonas palustris CGA009 through a genome-scale metabolic and expression model
Characterizing the interplay of rubisco 1 and nitrogenase enzymes in anaerobic-photoheterotrophically grown Rhodopseudomonas palustris CGA009 through a genome-scale metabolic and expression model
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通过基因组规模代谢和表达模型表征厌氧光异养生长的沼泽红假单胞菌 CGA009 中 rubisco 1 和固氮酶的相互作用
DOI：
10.1101/2022.03.03.482919
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Saha, R.
中科院分区：
文献类型：
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作者：
Chowdhury, Niaz B.;Alsiyabi, A.;Saha, R.
沼泽红假单胞菌 CGA009 是一种革兰氏阴性紫色非硫细菌，通过固定二氧化碳和氮进行光养生长，或者通过固定或分解代谢多种底物（包括用于其碳的木质素分解产物和固定氮以满足其氮需求）进行化养生长。它可以在需氧或厌氧条件下生长，并且可以利用光、无机和有机化合物来产生能量。由于其在厌氧生长过程中将不同碳源转化为有用产物的能力，本研究重建了沼泽红藻的代谢和表达（ME）模型，以研究其厌氧-光异养生长。与代谢 (M) 模型不同，ME 模型包括转录和翻译反应以及大分子合成，并将这些反应与生长速率结合起来。 ME 模型的这一独特特征导致了非线性增长曲线预测，与实验增长率数据密切匹配。在理论最大生长速率下，ME 模型表明碳固定速率递减，并预测苹果酸脱氢酶和 3 磷酸甘油脱氢酶作为替代电子汇。此外，ME 模型还确定铁氧还蛋白是在主要氧化还原平衡途径之间分配电子的关键调节剂。由于 ME 模型包括每个代谢反应的周转率，因此它被用来成功捕获实验观察到的不同固氮酶的温度调节。总体而言，ME 模型的这些独特特征证明了固氮酶和红糖对沼泽红菌生长的影响，并预测了在主要氧化还原平衡途径之间分配电子的关键调节因子，从而为从多组学角度对沼泽红菌代谢进行计算机研究建立了平台。重要性在这项工作中，我们重建了第一个紫色非硫细菌 (PNSB) 的 ME 模型。使用 ME 模型，对沼泽红藻代谢的不同方面进行了检查。首先，使用ME模型分析通过有机碳源进入沼泽沼泽菌细胞的还原能如何分配为生物量、二氧化碳固定和固氮。此外，ME 模型预测通过铁氧还蛋白的电子通量是向固氮酶分配电子的主要瓶颈。接下来，ME 模型表征了不同的固氮酶，并成功地重现了通过实验观察到的这些酶的温度调节。识别负责将电子转移到固氮酶的瓶颈并概括不同固氮酶的温度调节可能对代谢工程产生深远的影响，例如沼泽红藻的产氢。该 ME 模型的另一个有趣的应用是利用其氧化还原平衡策略来了解可生物降解塑料生产前体（例如聚羟基丁酸酯（PHB））的调节机制。
Rhodopseudomonas palustris CGA009 is a Gram-negative purple nonsulfur bacterium that grows phototrophically by fixing carbon dioxide and nitrogen or chemotrophically by fixing or catabolizing a wide array of substrates, including lignin breakdown products for its carbon and fixing nitrogen for its nitrogen requirements. It can grow aerobically or anaerobically and can use light, inorganic, and organic compounds for energy production. Due to its ability to convert different carbon sources into useful products during anaerobic growth, this study reconstructed a metabolic and expression (ME) model of R. palustris to investigate its anaerobic-photoheterotrophic growth. Unlike metabolic (M) models, ME models include transcription and translation reactions along with macromolecules synthesis and couple these reactions with growth rate. This unique feature of the ME model led to nonlinear growth curve predictions, which matched closely with experimental growth rate data. At the theoretical maximum growth rate, the ME model suggested a diminishing rate of carbon fixation and predicted malate dehydrogenase and glycerol-3 phosphate dehydrogenase as alternate electron sinks. Moreover, the ME model also identified ferredoxin as a key regulator in distributing electrons between major redox balancing pathways. Because ME models include the turnover rate for each metabolic reaction, it was used to successfully capture experimentally observed temperature regulation of different nitrogenases. Overall, these unique features of the ME model demonstrated the influence of nitrogenases and rubiscos on R. palustris growth and predicted a key regulator in distributing electrons between major redox balancing pathways, thus establishing a platform forin silicoinvestigation of R. palustris metabolism from a multiomics perspective.IMPORTANCEIn this work, we reconstructed the first ME model for a purple nonsulfur bacterium (PNSB). Using the ME model, different aspects of R. palustris metabolism were examined. First, the ME model was used to analyze how reducing power entering the R. palustris cell through organic carbon sources gets partitioned into biomass, carbon dioxide fixation, and nitrogen fixation. Furthermore, the ME model predicted electron flux through ferredoxin as a major bottleneck in distributing electrons to nitrogenase enzymes. Next, the ME model characterized different nitrogenase enzymes and successfully recapitulated experimentally observed temperature regulations of those enzymes. Identifying the bottleneck responsible for transferring an electron to nitrogenase enzymes and recapitulating the temperature regulation of different nitrogenase enzymes can have profound implications in metabolic engineering, such as hydrogen production from R. palustris. Another interesting application of this ME model can be to take advantage of its redox balancing strategy to gain an understanding of the regulatory mechanism of biodegradable plastic production precursors, such as polyhydroxybutyrate (PHB).