Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR
Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR
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DOI：
10.3389/fmicb.2018.02735
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发表时间：
2018-11-27
影响因子：
5.2
通讯作者：
Kaiyuzhnaya, Marina G.
中科院分区：
文献类型：
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作者：
Akberdin, Ilya R.;Collins, David A.;Kaiyuzhnaya, Marina G.
背景：稀土元素控制着甲烷和甲醇利用微生物对甲醇的利用。已经证实，稀土元素的加入导致MxaFI-MeDH（一种钙依赖的双亚基甲醇脱氢酶（MeDH））的转录抑制和XoxF-MeDH（一种镧依赖的单亚基甲醇脱氢酶）的激活。两种酶均为吡咯喹啉醌依赖醇脱氢酶，具有显著的同源性；然而，它们表现出不同的动力学性质和底物特异性。本研究在全球范围内研究了MxaFI到XoxF开关对代谢网络行为的影响。结果：本研究考察了甲基微生物alcaliphilum 20Z(R)在含钙（Ca）或镧（La，一种稀土元素）培养基中的稳态生长。我们发现，与ca培养相比，添加La的细胞具有更高的生长速度；然而，碳转化效率，估计为生物量产量，在Ca中生长的细胞中更高。三种互补的全球组学方法- rna -seq转录组学，蛋白质组学和代谢组学-被应用于研究改善生长与碳转化的机制。用La培养的细胞显示了xoxF基因的转录激活，xoxF基因是甲醛活化酶（fae2）的同源物，fae2是一种被认为的转运蛋白，血红蛋白转运蛋白基因和硝酸盐还原酶。相反，mxaFI基因和相关细胞色素（mxaG）表达下调。蛋白质组学分析表明，在蛋白质水平上，代谢网络有额外的调整，包括碳同化途径、电子传递系统和三羧酸（TCA）循环。基因表达和蛋白质丰度变化之间的不一致指向了相关系统转录后控制的可能性，包括TCA循环的关键酶和一组电子传递载体。代谢组学数据遵循蛋白质组学，显示RuMP途径中间体减少，TCA循环代谢物增加。结论：与补充Ca的细胞相比，暴露于REEs的细胞表现出更高的生长速度，但碳转化效率较低。对这些生理变化最合理的解释是XoxF-MeDH增加了甲醇转化为甲酸，这进一步刺激了甲烷氧化，但限制了还原能力的供应和甲醛进入RuMP途径的通量。
Background: Rare Earth Elements (REEs) control methanol utilization in both methane- and methanol-utilizing microbes. It has been established that the addition of REEs leads to the transcriptional repression of MxaFI-MeDH [a two-subunit methanol dehydrogenase (MeDH), calcium-dependent] and the activation of XoxF-MeDH (a one-subunit MeDH, lanthanum-dependent). Both enzymes are pyrroquinoline quinone-dependent alcohol dehydrogenases and show significant homology; however, they display different kinetic properties and substrate specificities. This study investigates the impact of the MxaFI to XoxF switch on the behavior of metabolic networks at a global scale.Results: In this study we investigated the steady-state growth of Methylomicrobium alcaliphilum 20Z(R) in media containing calcium (Ca) or lanthanum (La, a REE element). We found that cells supplemented with La show a higher growth rate compared to Ca-cultures; however, the efficiency of carbon conversion, estimated as biomass yield, is higher in cells grown with Ca. Three complementary global-omics approachesRNA-seq transcriptomics, proteomics, and metabolomics-were applied to investigate the mechanisms of improved growth vs. carbon conversion. Cells grown with La showed the transcriptional activation of the xoxF gene, a homolog of the formaldehyde-activating enzyme (fae2), a putative transporter, genes for hemin-transport proteins, and nitrate reductase. In contrast, genes for mxaFI and associated cytochrome (mxaG) expression were downregulated. Proteomic profiling suggested additional adjustments of the metabolic network at the protein level, including carbon assimilation pathways, electron transport systems, and the tricarboxylic acid (TCA) cycle. Discord between gene expression and protein abundance changes points toward the possibility of post-transcriptional control of the related systems including key enzymes of the TCA cycle and a set of electron-transport carriers. Metabolomic data followed proteomics and showed the reduction of the ribulose-monophosphate (RuMP) pathway intermediates and the increase of the TCA cycle metabolites.Conclusion: Cells exposed to REEs display higher rates of growth but have lower carbon conversion efficiency compared to cells supplemented with Ca. The most plausible explanation for these physiological changes is an increased conversion of methanol into formate by XoxF-MeDH, which further stimulates methane oxidation but limits both the supply of reducing power and flux of formaldehyde into the RuMP pathway.