A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.
A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.
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DOI：
10.1101/gr.153916.112
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发表时间：
2013-11
期刊：
影响因子：
7
通讯作者：
Baliga NS
中科院分区：
文献类型：
--
作者：
Yoon SH;Turkarslan S;Reiss DJ;Pan M;Burn JA;Costa KC;Lie TJ;Slagel J;Moritz RL;Hackett M;Leigh JA;Baliga NS
产甲烷菌催化有机物厌氧分解中关键的产甲烷步骤（称为产甲烷）。在这里，我们提出了氢营养型产甲烷菌（Methanococcus maripaludis）产甲烷作用的全球基因调控的第一个预测模型。我们通过转录组结构的综合分析和新构建的肽图谱生成了 M. maripaludis 的基因（蛋白质编码和非编码）的全面列表。该菌株的环境和基因调控影响网络 (EGRIN) 模型是根据转录组数据概要构建的，这些数据收集了超过 58 个不同的稳态和时间过程实验，这些实验是在调节产甲烷作用的一系列环境扰动下在恒化器或分批培养物中进行的。 EGRIN 模型的分析揭示了产甲烷作用的新组成部分，其中包括至少三个以前未知功能的额外蛋白质编码基因以及一种非编码 RNA。我们发现至少有五种调节机制以组合方式发挥作用，以协调产甲烷的关键步骤与不同过程（例如运动性、ATP 生物合成和碳同化）。通过结合遗传和环境扰动实验，我们验证了 EGRIN 预测的两种新型转录因子在磷酸盐依赖性抑制甲酸脱氢酶（产甲烷途径中的关键酶）的调节中的作用。 EGRIN 模型展示了产甲烷过程中以及产甲烷过程与其他细胞功能之间的调节关系。
Methanogens catalyze the critical methane-producing step (called methanogenesis) in the anaerobic decomposition of organic matter. Here, we present the first predictive model of global gene regulation of methanogenesis in a hydrogenotrophic methanogen, Methanococcus maripaludis. We generated a comprehensive list of genes (protein-coding and noncoding) for M. maripaludis through integrated analysis of the transcriptome structure and a newly constructed Peptide Atlas. The environment and gene-regulatory influence network (EGRIN) model of the strain was constructed from a compendium of transcriptome data that was collected over 58 different steady-state and time-course experiments that were performed in chemostats or batch cultures under a spectrum of environmental perturbations that modulated methanogenesis. Analyses of the EGRIN model have revealed novel components of methanogenesis that included at least three additional protein-coding genes of previously unknown function as well as one noncoding RNA. We discovered that at least five regulatory mechanisms act in a combinatorial scheme to intercoordinate key steps of methanogenesis with different processes such as motility, ATP biosynthesis, and carbon assimilation. Through a combination of genetic and environmental perturbation experiments we have validated the EGRIN-predicted role of two novel transcription factors in the regulation of phosphate-dependent repression of formate dehydrogenase—a key enzyme in the methanogenesis pathway. The EGRIN model demonstrates regulatory affiliations within methanogenesis as well as between methanogenesis and other cellular functions.
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DOI：
10.1073/pnas.0701157104
发表时间：
2007-05-22
影响因子：
11.1
作者：
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影响因子：
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影响因子：
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作者：
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DOI：
10.1073/pnas.1016761108
发表时间：
2011-02-15
影响因子：
11.1
作者：
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DOI：
10.1073/pnas.97.21.11522
发表时间：
2000-10-10
影响因子：
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作者：
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