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微重力对拟南芥长势影响的代谢网络流平衡分析

王芷涵 阮耀 张青叶 张红雨

王芷涵, 阮耀, 张青叶, 张红雨. 微重力对拟南芥长势影响的代谢网络流平衡分析[J]. 空间科学学报. doi: 10.11728/cjss2022.05.210714077
引用本文: 王芷涵, 阮耀, 张青叶, 张红雨. 微重力对拟南芥长势影响的代谢网络流平衡分析[J]. 空间科学学报. doi: 10.11728/cjss2022.05.210714077
WANG Zhihan, RUAN Yao, ZHANG Qingye, ZHANG Hongyu. Metabolic Network Flux Balance Analysis of the Microgravity Influence on the Growth of Arabidopsis Thaliana (in Chinese). Chinese Journal of Space Science, xxxx, x(x): x-xx doi: 10.11728/cjss2022.05.210714077
Citation: WANG Zhihan, RUAN Yao, ZHANG Qingye, ZHANG Hongyu. Metabolic Network Flux Balance Analysis of the Microgravity Influence on the Growth of Arabidopsis Thaliana (in Chinese). Chinese Journal of Space Science, xxxx, x(x): x-xx doi: 10.11728/cjss2022.05.210714077

微重力对拟南芥长势影响的代谢网络流平衡分析

doi: 10.11728/cjss2022.05.210714077
基金项目: 国家自然科学基金面上项目资助(31870837)
详细信息
    作者简介:

    张青叶:E-mail:zqy@mail.hzau.edu.cnzqy@mail.hzau.edu.cn

Metabolic Network Flux Balance Analysis of the Microgravity Influence on the Growth of Arabidopsis Thaliana

  • 摘要: 微重力作为典型的空间环境因素,对植物生长发育的影响机制是空间生命科学的研究热点。微重力环境直接或间接影响植物代谢,并引起许多生理适应。 随着系统生物学的发展,代谢网络模型使微重力环境下的植物代谢建模成为可能。采用流平衡分析方法对模式植物拟南芥不同组织的代谢网络进行分析,研究微重力对拟南芥生长发育的影响机制。通过比较空间与地面条件下拟南芥的生物质产量,发现空间条件下拟南芥黄化幼苗、幼苗、芽、根、下胚轴的生物量分别下降了33.00%、51.52%、6.89%、12.53%、11.70%,与空间环境下拟南芥的长势变化趋势一致。代谢通路富集分析发现,微重力使得拟南芥的碳固定等通路下调,而磷酸戊糖途径上调,初步解析了微重力对拟南芥生长发育的影响机制,也验证了流平衡方法用于微重力生物学效应研究中的可行性。

     

  • 图  1  拟南芥黄化幼苗(a)、幼苗(b)、芽(c)、根(d)和下胚轴(e)在微重力与地面环境下的生物质产量以及ATP相关反应的通量对比. 纵坐标表示反应速率,毫摩尔每克(干重)每小时。横坐标为生物量及产生ATP的反应

    Figure  1.  Mustard biomass production and ATP synthesis reaction fluxes of Arabidopsis thaliana etiolated seedlings (a), seedlings (b), shoots (c), roots (d), and hypocotyls (e) in microgravity and ground environment. The ordinate is the reaction rate, millimole per gram (dry weight) per hour. The abscissa is the reaction of biomass and ATP.

    表  1  拟南芥黄化幼苗下调反应对应基因的富集途径

    Table  1.   Enrichment pathways for genes corresponding to Arabidopsis thaliana etiolated seedlings down-regulation responses

    通路KEGG通路IDpFDR
    Glyoxylate and dicarboxylate metabolismath006304.24×10–241.10×10–22
    Carbon metabolismath012001.88×10–162.44×10–15
    Biosynthesis of antibioticsath011302.20×10–111.91×10–10
    Metabolic pathwaysath011004.68×10–113.04×10–10
    Biosynthesis of secondary metabolitesath011106.97×10–103.62×10–9
    Carbon fixation in photosynthetic organismsath007101.21×10–95.24×10–9
    Pyruvate metabolismath006206.00×10–92.23×10–8
    Citrate cycle (TCA cycle)ath000202.12×10–86.88×10–8
    Cysteine and methionine metabolismath002705.04×10–71.46×10–6
    One carbon pool by folateath006702.79×10–67.24×10–6
    下载: 导出CSV

    表  2  拟南芥幼苗下调反应对应基因的富集途径

    Table  2.   Enrichment pathways for genes corresponding to Arabidopsis thaliana seedlings down-regulation responses

    通路KEGG通路IDpFDR
    Oxidative phosphorylationath001903.16×10–259.49×10–24
    Metabolic pathwaysath011002.24×10–243.36×10–23
    Biosynthesis of amino acidsath012307.08×10–247.08×10–23
    Phenylalanine, tyrosine and tryptophan biosynthesisath004003.60×10–162.70×10–15
    Carbon fixation in photosynthetic organismsath007101.82×10–151.09×10–14
    Biosynthesis of secondary metabolitesath011101.96×10–129.82×10–12
    Biosynthesis of antibioticsath011301.12×10–104.79×10–10
    Phagosomeath041451.81×10–106.78×10–10
    Carbon metabolismath012002.82×10–109.40×10–10
    Nitrogen metabolismath009105.95×10–91.79×10–8
    下载: 导出CSV

    表  3  拟南芥芽下调反应对应基因的富集途径

    Table  3.   Enrichment pathways for genes corresponding to Arabidopsis thaliana shoot down-regulation responses

    通路KEGG通路IDpFDR
    Carbon metabolismath012008.48×10–441.36×10–42
    Biosynthesis of antibioticsath011305.95×10–404.76×10–39
    Pentose phosphate pathwayath000302.01×10–351.07×10–34
    Glycolysis / Gluconeogenesisath000102.27×10–339.09×10–33
    Carbon fixation in photosynthetic organismsath007102.20×10–287.05×10–28
    Biosynthesis of secondary metabolitesath011102.04×10–235.43×10–23
    Metabolic pathwaysath011003.75×10–168.58×10–16
    Fructose and mannose metabolismath000511.05×10–132.10×10–13
    Nitrogen metabolismath009103.26×10–135.79×10–13
    Biosynthesis of amino acidsath012304.02×10–126.43×10–12
    下载: 导出CSV

    表  4  拟南芥根下调反应对应基因的富集途径

    Table  4.   Enrichment pathways for genes corresponding to Arabidopsis thaliana root down-regulation responses

    通路KEGG通路IDpFDR
    Carbon metabolismath012003.50×10–354.20×10–34
    Carbon fixation in photosynthetic organismsath007101.42×10–348.53×10–34
    Glycolysis / Gluconeogenesisath000101.63×10–236.53×10–23
    Biosynthesis of amino acidsath012301.16×10–223.48×10–22
    Biosynthesis of antibioticsath011302.89×10–206.94×10–20
    Metabolic pathwaysath011005.74×10–191.15×10–18
    Pentose phosphate pathwayath000308.53×10–131.46×10–12
    Fructose and mannose metabolismath000514.30×10–126.45×10–12
    Biosynthesis of secondary metabolitesath011103.44×10–114.58×10–11
    Arginine biosynthesisath002205.65×10–106.78×10–10
    下载: 导出CSV

    表  5  拟南芥下胚轴下调反应对应基因的富集途径

    Table  5.   Enrichment pathways for genes corresponding to Arabidopsis thaliana hypocotyl down-regulation responses

    通路KEGG通路IDpFDR
    Carbon fixation in photosynthetic organismsath007101.05×10–301.48×10–29
    Carbon metabolismath012001.40×10–289.80×10–28
    Glycolysis / Gluconeogenesisath000103.94×10–231.84×10–22
    Biosynthesis of antibioticsath011301.33×10–204.66×10–20
    Biosynthesis of secondary metabolitesath011101.25×10–193.49×10–19
    Metabolic pathwaysath011003.46×10–188.08×10–18
    Fructose and mannose metabolismath000512.05×10–154.10×10–15
    Biosynthesis of amino acidsath012301.42×10–142.48×10–14
    Pentose phosphate pathwayath000301.95×10–133.03×10–13
    Arginine biosynthesisath002207.01×10–109.82×10–10
    下载: 导出CSV

    表  6  拟南芥黄化幼苗上调反应对应基因的富集途径

    Table  6.   Enrichment pathways for genes corresponding to Arabidopsis thaliana etiolated seedlings up-regulation responses

    通路KEGG通路IDpFDR
    Carbon metabolismath012003.78×10–374.16×10–36
    Biosynthesis of antibioticsath011309.37×10–225.15×10–21
    Pentose phosphate pathwayath000304.01×10–181.47×10–17
    Carbon fixation in photosynthetic organismsath007106.44×10–181.77×10–17
    Nitrogen metabolismath009101.45×10–113.18×10–11
    Biosynthesis of secondary metabolitesath011102.22×10–114.07×10–11
    Biosynthesis of amino acidsath012309.14×10–111.44×10–10
    Metabolic pathwaysath011001.76×10–92.42×10–9
    Glycolysis / Gluconeogenesisath000103.36×10–74.11×10–7
    Glutathione metabolismath004807.11×10–67.82×10–6
    下载: 导出CSV

    表  7  拟南芥幼苗上调反应对应基因的富集途径

    Table  7.   Enrichment pathways for genes corresponding to Arabidopsis thaliana seedlings up-regulation responses

    通路KEGG通路IDpFDR
    Carbon metabolismath012001.85×10–231.37×10–22
    Pentose phosphate pathwayath000302.28×10–231.37×10–22
    Biosynthesis of antibioticsath011305.24×10–232.10×10–22
    Biosynthesis of secondary metabolitesath011102.05×10–206.14×10–20
    Metabolic pathwaysath011003.38×10–158.12×10–15
    Phenylalanine metabolismath003601.27×10–82.55×10–8
    Citrate cycle (TCA cycle)ath000202.06×10–83.53×10–8
    Carbon fixation in photosynthetic organismsath007109.38×10–61.41×10–5
    Glycolysis / Gluconeogenesisath000103.01×10–54.01×10–5
    下载: 导出CSV

    表  8  拟南芥芽上调反应对应基因的富集途径

    Table  8.   Enrichment pathways for genes corresponding to Arabidopsis thaliana shoot up-regulation responses.

    通路KEGG通路IDpFDR
    Oxidative phosphorylationath001904.27×10–475.98×10–46
    Phagosomeath041451.45×10–181.02×10–17
    Metabolic pathwaysath011005.92×10–122.76×10–11
    Ascorbate and aldarate metabolismath000531.25×10–44.37×10–4
    One carbon pool by folateath006700.0017230.004825
    下载: 导出CSV

    表  9  拟南芥根上调反应对应基因的富集途径

    Table  9.   Enrichment pathways for genes corresponding to Arabidopsis thaliana root up-regulation responses

    通路KEGG通路IDpFDR
    Oxidative phosphorylationath001903.63×10–321.02×10–30
    Metabolic pathwaysath011002.07×10–252.90×10–24
    Biosynthesis of secondary metabolitesath011101.85×10–181.73×10–17
    Biosynthesis of amino acidsath012303.81×10–152.67×10–14
    Biosynthesis of antibioticsath011306.91×10–153.87×10–14
    Citrate cycle (TCA cycle)ath000201.77×10–148.24×10–14
    Phenylalanine, tyrosine and tryptophan biosynthesisath004005.69×10–132.27×10–12
    2-Oxocarboxylic acid metabolismath012105.91×10–112.07×10–10
    Phagosomeath041456.69×10–112.08×10–10
    Phenylalanine metabolismath003602.09×10–105.84×10–10
    下载: 导出CSV

    表  10  拟南芥下胚轴上调反应对应基因的富集途径

    Table  10.   Enrichment pathways for genes corresponding to Arabidopsis thaliana hypocotyl up-regulation responses

    通路KEGG通路IDpFDR
    Glyoxylate and dicarboxylate metabolismath006301.12×10–211.23×10–20
    Nitrogen metabolismath009102.19×10–201.21×10–19
    Carbon metabolismath012007.92×10–92.91×10–8
    Carbon fixation in photosynthetic organismsath007105.85×10–81.61×10–7
    Alanine, aspartate and glutamate metabolismath002508.51×10–81.87×10–7
    Pyruvate metabolismath006202.79×10–75.12×10–7
    One carbon pool by folateath006704.16×10–76.53×10–7
    Citrate cycle (TCA cycle)ath000205.85×10–78.04×10–7
    Biosynthesis of antibioticsath011308.07×10–79.86×10–7
    Cysteine and methionine metabolismath002701.27×10–51.40×10–5
    下载: 导出CSV
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  • 收稿日期:  2021-07-14
  • 录用日期:  2022-04-12
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  • 网络出版日期:  2022-09-17

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