Genome-wide transcriptome profiling of nitrogen fixation in Paenibacillus sp. WLY78.
Genome-wide transcriptome profiling of nitrogen fixation in Paenibacillus sp. WLY78.
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类芽孢杆菌 WLY78 固氮的全基因组转录组分析
DOI：
10.1186/s12866-016-0642-6
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发表时间：
2016-03-01
期刊：
影响因子：
4.2
通讯作者：
Chen SF
中科院分区：
文献类型：
--
作者：
Shi HW;Wang LY;Li XX;Liu XM;Hao TY;He XJ;Chen SF
固氮（固氮）革兰氏阳性和内孢子形成类芽孢杆菌属。在农业上作为细菌肥料具有潜在的用途。类芽孢杆菌固氮的转录分析是缺乏的，虽然固氮的调控机制已在革兰氏阴性固氮菌进行了充分的研究。在这里，我们报告了一个整体的转录谱分析固氮类芽孢杆菌属物种WLY 78培养下的N2固定条件（无O2和NH 4+）和非N2固定条件（空气和100 mM NH 4+）。该菌由9个基因（nifBHDKENXhesAnifV）组成的nif基因操纵子在固氮条件下的表达量显著高于非固氮条件，表明nif基因的转录受NH 4+和O2的严格控制。qRT-PCR证实了这些nif基因的差异表达。在固氮条件下，非nif基因，如mod、feoAB和cys等编码Mo、Fe和S原子转运蛋白的基因与nif基因协同转录。在固氮条件下，合成Fe-S簇的suf操纵子的转录丰度上调，表明Sul系统取代nifS和nifU在固氮酶合成中起重要作用。我们发现了固氮酶的铁蛋白向钼铁蛋白提供电子的潜在的特异性电子转运蛋白。GlnR在固氮条件下表达显著上调，其预测蛋白可能介导NH 4+对nif转录的调控。分析了氮代谢和无氧呼吸的转录水平。类芽孢杆菌WLY 78的nif基因操纵子（nifBHDKENXhesAnifV）在固氮条件下比非固氮条件下显著上调。固氮所需的非nif基因在固氮条件下也显著上调。固氮条件下，参与厌氧调控的Fur和Fnr以及可能介导NH 4+对nif基因转录调控的GlnR表达显著上调。本研究为了解革兰氏阳性厚壁菌的固氮过程及其调控提供了有价值的信息。本文的在线版本（doi：10.1186/s12866-016-0642-6）包含补充材料，可供授权用户使用。
Diazotrophic (nitrogen-fixing) Gram-positive and endospore-formed Paenibacillus spp. have potential uses as a bacterial fertilizer in agriculture. The transcriptional analysis of nitrogen fixation in Paenibacillus is lacking, although regulation mechanisms of nitrogen fixation have been well studied in Gram-negative diazotrophs. Here we report a global transcriptional profiling analysis of nitrogen fixation in Paenibacillus sp. WLY78 cultured under N2-fixing condition (without O2 and NH4+) and non-N2-fixing condition (air and 100 mM NH4+). The nif (nitrogen fixation) gene operon composed of 9 genes (nifBHDKENXhesAnifV) in this bacterium was significantly up-regulated in N2-fixing condition compared to non-N2-fixing condition, indicating that nif gene transcription is strictly controlled by NH4+ and O2. qRT-PCR confirmed that these nif genes were differently expressed. Non-nif genes specifically required in nitrogen fixation, such as mod, feoAB and cys encoding transporters of Mo, Fe and S atoms, were coordinately transcribed with nif genes in N2-fixing condition. The transcript abundance of suf operon specific for synthesis of Fe-S cluster was up-regulated in N2-fixing condition, suggesting that Sul system, which takes place of nifS and nifU, plays important role in the synthesis of nitrogenase. We discover potential specific electron transporters which might provide electron from Fe protein to MoFe protein of nitrogenase. The glnR whose predicted protein might mediate nif transcription regulation by NH4+ is significantly up-regulated in N2-fixing condition. The transcription levels of nitrogen metabolism and anaerobic respiration were also analyzed. The nif gene operon (nifBHDKENXhesAnifV) in Paenibacillus sp. WLY78 is significantly up-regulated in N2-fixing condition compared to non-N2-fixing condition. Non-nif genes specifically required in nitrogen fixation were also significantly up-regulated in N2-fixing condition. Fur and Fnr which are involved in anaerobic regulation and GlnR which might mediate nif gene transcription regulation by NH4+ were significantly up-regulated in N2-fixing condition. This study provides valuable insights into nitrogen fixation process and regulation in Gram-positive firmicutes. The online version of this article (doi:10.1186/s12866-016-0642-6) contains supplementary material, which is available to authorized users.