Campos Diego Tec, Zuñiga Cristal, Passi Anurag, Del Toro John, Tibocha-Bonilla Juan D, Zepeda Alejandro, Betenbaugh Michael J, Zengler Karsten
Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.
Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico.
Metab Eng Commun. 2020 May 30;11:e00132. doi: 10.1016/j.mec.2020.e00132. eCollection 2020 Dec.
Nitrogen fixation is an important metabolic process carried out by microorganisms, which converts molecular nitrogen into inorganic nitrogenous compounds such as ammonia (NH). These nitrogenous compounds are crucial for biogeochemical cycles and for the synthesis of essential biomolecules, i.e. nucleic acids, amino acids and proteins. is a bacterial non-photosynthetic model organism to study aerobic nitrogen fixation (diazotrophy) and hydrogen production. Moreover, the diazotroph can produce biopolymers like alginate and polyhydroxybutyrate (PHB) that have important industrial applications. However, many metabolic processes such as partitioning of carbon and nitrogen metabolism in remain unknown to date. Genome-scale metabolic models (M-models) represent reliable tools to unravel and optimize metabolic functions at genome-scale. M-models are mathematical representations that contain information about genes, reactions, metabolites and their associations. M-models can simulate optimal reaction fluxes under a wide variety of conditions using experimentally determined constraints. Here we report on the development of a M-model of the wild type bacterium DJ (DT1278) which consists of 2,003 metabolites, 2,469 reactions, and 1,278 genes. We validated the model using high-throughput phenotypic and physiological data, testing 180 carbon sources and 95 nitrogen sources. DT1278 was able to achieve an accuracy of 89% and 91% for growth with carbon sources and nitrogen source, respectively. This comprehensive M-model will help to comprehend metabolic processes associated with nitrogen fixation, ammonium assimilation, and production of organic nitrogen in an environmentally important microorganism.
固氮作用是微生物进行的一个重要代谢过程，它将分子态氮转化为无机含氮化合物，如氨（NH）。这些含氮化合物对于生物地球化学循环以及必需生物分子（即核酸、氨基酸和蛋白质）的合成至关重要。[具体细菌名称]是一种用于研究好氧固氮（固氮作用）和产氢的非光合细菌模式生物。此外，这种固氮菌能够产生具有重要工业应用价值的生物聚合物，如藻酸盐和聚羟基丁酸酯（PHB）。然而，到目前为止，[具体细菌名称]中许多代谢过程，如碳氮代谢的分配仍不清楚。基因组尺度代谢模型（M模型）是揭示和优化基因组尺度代谢功能的可靠工具。M模型是一种数学表示，包含有关基因、反应、代谢物及其关联的信息。M模型可以使用实验确定的约束条件，在各种条件下模拟最佳反应通量。在此，我们报告了野生型细菌[具体细菌名称] DJ（DT1278）的M模型的构建，该模型由2003种代谢物、2469个反应和1278个基因组成。我们使用高通量表型和生理数据验证了该模型，测试了180种碳源和95种氮源。DT1278在利用碳源和氮源生长方面的预测准确率分别达到了89%和91%。这个全面的M模型将有助于理解一种对环境具有重要意义的微生物中与固氮作用、铵同化和有机氮产生相关的代谢过程。
