Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803.
Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803.
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DOI：
10.1371/journal.pcbi.1003081
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发表时间：
2013
影响因子：
4.3
通讯作者：
Steuer R
中科院分区：
文献类型：
--
作者：
Knoop H;Gründel M;Zilliges Y;Lehmann R;Hoffmann S;Lockau W;Steuer R
蓝细菌是多功能单细胞光养微生物，在许多环境中含量很高。由于蓝藻能够利用太阳能和大气二氧化碳进行生长，因此越来越多地被认为是合成有价值的化学品和各种生物燃料的丰富资源。为了充分利用蓝藻的代谢能力，需要深入了解光养生长过程中发生的代谢相互转化，正如微生物的基因组规模重建所提供的那样。在这里，我们对单细胞蓝藻集胞藻的代谢网络进行了扩展重建和分析。 PCC 6803。基于最近对蓝藻代谢的几个重建，通过实验验证了不清楚的反应步骤，并讨论了未知或不同途径拓扑的功能后果。更新后的模型整合了有关蓝藻 TCA 循环、所谓的乙醛酸分流以及光呼吸在细胞生长中的作用的新结果。超越传统的通量平衡分析，我们将计算分析扩展到蓝藻代谢的昼夜光/暗循环。光养微生物作为一种资源，仅利用大气中的二氧化碳、光和一些矿物质即可生产高价值产品和生物燃料，具有广阔的前景。特别是蓝细菌，唯一已知的能够进行光合作用放氧的原核生物，最近作为产生第三代生物燃料的可能基础而引起了人们的关注。微生物的合理工程越来越受到相应生物体代谢网络大规模重建的指导。然后，这种重建可以作为细胞生长过程中发生的所有代谢相互转化的综合知识库。在这里，我们提出并分析了单细胞蓝藻集胞藻属的基因组规模重建。 PCC 6803。考虑到最近的几次重建，讨论了不清楚和不一致的途径注释的功能后果。该模型补充了实验数据以验证特定的反应步骤。作为光养生物的一个具体特征，研究了昼夜光/暗交替循环中新陈代谢的重组。
Cyanobacteria are versatile unicellular phototrophic microorganisms that are highly abundant in many environments. Owing to their capability to utilize solar energy and atmospheric carbon dioxide for growth, cyanobacteria are increasingly recognized as a prolific resource for the synthesis of valuable chemicals and various biofuels. To fully harness the metabolic capabilities of cyanobacteria necessitates an in-depth understanding of the metabolic interconversions taking place during phototrophic growth, as provided by genome-scale reconstructions of microbial organisms. Here we present an extended reconstruction and analysis of the metabolic network of the unicellular cyanobacterium Synechocystis sp. PCC 6803. Building upon several recent reconstructions of cyanobacterial metabolism, unclear reaction steps are experimentally validated and the functional consequences of unknown or dissenting pathway topologies are discussed. The updated model integrates novel results with respect to the cyanobacterial TCA cycle, an alleged glyoxylate shunt, and the role of photorespiration in cellular growth. Going beyond conventional flux-balance analysis, we extend the computational analysis to diurnal light/dark cycles of cyanobacterial metabolism. Phototrophic microorganisms hold great promises as a resource to generate high-value products and biofuels using only atmospheric carbon dioxide, light, and some minerals. In particular cyanobacteria, the only known prokaryotes capable of oxygen-evolving photosynthesis, have attracted recent attention as a possible chassis for the generation of third generation biofuels. Rational engineering of microorganisms is increasingly guided by large-scale reconstructions of the metabolic network of the respective organism. Such reconstructions then serve as an integrated knowledge base for all metabolic interconversions taking place during cellular growth. Here, we present and analyze such a genome-scale reconstruction for the unicellular cyanobacterium Synechocystis sp. PCC 6803. Taking into account several recent reconstructions, the functional consequences of unclear and dissenting pathway annotations are discussed. The model is supplemented with experimental data to validate specific reactions steps. As a specific feature of phototrophic organisms, the re-organization of metabolism in alternating diurnal light/dark cycles is studied.
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影响因子：
3.5
作者：
Cerveny, Jan;Nedbal, Ladislav
通讯作者：
Nedbal, Ladislav
FASIMU：大型代谢网络中通量平衡计算系列的灵活软件。
影响因子：
3
作者：
Hoppe A;Hoffmann S;Gerasch A;Gille C;Holzhütter HG
通讯作者：
Holzhütter HG
影响因子：
9.2
作者：
Helman, Y;Tchernov, D;Kaplan, A
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影响因子：
6.4
作者：
Bandyopadhyay A;Elvitigala T;Welsh E;Stöckel J;Liberton M;Min H;Sherman LA;Pakrasi HB
通讯作者：
Pakrasi HB
影响因子：
3.7
作者：
Hamilton, Joshua J.;Reed, Jennifer L.
通讯作者：
Reed, Jennifer L.