生物技术通报 ›› 2022, Vol. 38 ›› Issue (2): 10-20.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0542
李兵娟1,2(), 郑璐1, 沈仁芳1,2, 兰平1,2()
收稿日期:
2021-04-23
出版日期:
2022-02-26
发布日期:
2022-03-09
作者简介:
李兵娟,女,博士研究生,研究方向:植物营养蛋白质组学;E-mail: 基金资助:
LI Bing-juan1,2(), ZHENG Lu1, SHEN Ren-fang1,2, LAN Ping1,2()
Received:
2021-04-23
Published:
2022-02-26
Online:
2022-03-09
摘要:
核糖体蛋白不仅参与蛋白质合成,而且参与植物生长发育的调控。利用拟南芥核糖体磷酸蛋白P1(ribosomal phosphoprotein P1,RPP1)家族基因RPP1A缺失突变体rpp1a研究RPP1A缺失对幼苗蛋白质表达水平的影响,揭示其参与调控幼苗生长的作用机制。表型分析发现,与野生型WT相比,RPP1A缺失导致拟南芥幼苗生物量、叶片总表面积和叶柄长度显著增加。基于label-free的蛋白质组学分析,与野生型相比,rpp1a-2突变体有280个蛋白质表达量具有显著差异,其中98个显著上调,182个显著下调。差异蛋白主要富集在细胞过程、代谢过程、刺激反应、细胞成分组织或生物发生和氧化还原过程等生物学过程,并在核糖体、光合作用、mRNA监视途径、RNA降解和苯丙素的生物合成代谢通路中显著富集。拟南芥rpp1a-2突变体通过抑制刺激反应和增强光合作用等过程促进植物生长。
李兵娟, 郑璐, 沈仁芳, 兰平. 拟南芥RPP1A参与幼苗生长的蛋白质组学分析[J]. 生物技术通报, 2022, 38(2): 10-20.
LI Bing-juan, ZHENG Lu, SHEN Ren-fang, LAN Ping. Proteomic Analysis of RPP1A Involved in the Seedling Growth of Arabidopsis thaliana[J]. Biotechnology Bulletin, 2022, 38(2): 10-20.
图1 拟南芥WT和rpp1a-1和rpp1a-2突变体幼苗表型 拟南芥WT和rpp1a-1和rpp1a-2突变体在ES培养基上生长14 d的幼苗表型(A)和幼苗鲜重(B)、叶片表型(C)、叶片总表面积(D)和叶柄长度(E)。数值以±s差表示,采用one-way ANOVA检验进行显著性分析,***表示极显著差异(P<0.001)
Fig. 1 Seedling phenotypes of Arabidopsis thaliana WT and rpp1a-1 and rpp1a-2 mutants Phenotype of seedlings(A),fresh weight(B),leaf phenotype(C),total leaf surface area(D),and length of petioles(E)of Arabidopsis thaliana WT and rpp1a-1 and rpp1a-2 mutants growing on ES medium for 14 d. Values are expressed as ±s deviation,and a one-way ANOVA test is used for significance analysis. *** refers to extremely significant difference(P<0.001)
拟南芥基因号 AGI locus ID | 蛋白质名称 Protein name | 描述 Description | 丰度比Abundance ratio | 丰度比的调整P值 Abundance ratio adj. P value | 丰度比变异性 Abundance ratio variability/% |
---|---|---|---|---|---|
核糖体Ribosome | |||||
AT3G49080 | RPS9M | 核糖体蛋白S9 M Ribosomal protein S9 M | 100.00 | 2.02E-16 | 0.00 |
AT2G21580 | RPS25B | 核糖体蛋白S25家族蛋白 Ribosomal protein S25 family protein | 11.39 | 2.02E-16 | 642.26 |
AT2G19740 | RPL31A | 核糖体蛋白L31e家族蛋白 Ribosomal protein L31e family protein | 0.63 | 3.50E-02 | 7.21 |
AT5G56670 | RPS30C | 核糖体蛋白S30家族蛋白 Ribosomal protein S30 family protein | 0.59 | 4.08E-02 | 3.33 |
AT3G46040 | RPS15aD | 核糖体蛋白S15a D Ribosomal protein S15a D | 0.58 | 2.65E-02 | 1.03 |
AT5G16130 | RPS7C | 核糖体蛋白S7e家族蛋白 Ribosomal protein S7e family protein | 0.57 | 8.83E-04 | 2.09 |
AT1G04270 | RPS15A | 核糖体蛋白S15 Ribosomal protein S15 | 0.53 | 6.16E-03 | 14.83 |
AT5G18380 | RPS16C | 核糖体蛋白S5结构域2类似超家族蛋白Ribosomal protein S5 domain 2-like superfamily protein | 0.51 | 1.27E-04 | 8.10 |
AT5G23900 | RPL13D | 核糖体蛋白L13e家族蛋白 Ribosomal protein L13e family protein | 0.49 | 1.49E-04 | 4.12 |
AT2G27720 | RPP2A | 60S酸性核糖体蛋白家族 60S acidic ribosomal protein family | 0.43 | 1.14E-05 | 1.49 |
AT3G28900 | RPL34C | 核糖体蛋白L34e超家族蛋白质 Ribosomal protein L34e superfamily protein | 0.33 | 1.77E-04 | 2.55 |
AT1G01100 | RPP1A | 60S酸性核糖体蛋白家族 60S acidic ribosomal protein family | 0.01 | 2.02E-16 | 0.00 |
光合作用Photosynthesis | |||||
ATCG00020 | PSBA | 光系统II反应中心蛋白D1 Phot-osystem II reaction center protein D1 | 1.75 | 6.17E-04 | 18.27 |
ATCG00270 | PSBD | P光系统II反应中心蛋白D2 Pho-tosystem II reaction center protein D2 | 1.69 | 1.53E-03 | 16.06 |
ATCG00580 | PSBE | 光系统II反应中心蛋白V Phot-osystem II reaction center protein V | 0.62 | 3.90E-02 | 7.74 |
ATCG00470 | ATPE | ATP合酶ε亚基 ATP synthase epsilon subunit | 0.58 | 1.20E-02 | 4.17 |
AT1G10960 | FD1 | 铁氧还原蛋白1 Ferredoxin 1 | 0.01 | 2.02E-16 | 0.00 |
mRNA监视通路mRNA surveillance pathway | |||||
AT1G13320 | PP2AA3 | 蛋白磷酸酶2A亚基A3 Protein phosphatase 2A subunit A3 | 100.00 | 2.02E-16 | 0.00 |
AT1G02140 | MAGO | Mago nashi家族蛋白 Mago nashi family protein | 2.23 | 1.48E-05 | 20.68 |
AT1G17720 | ATB BETA | 蛋白磷酸酶2A,调控亚基PR55 Protein phosphatase 2A,regulatory subunit PR55 | 0.13 | 1.44E-12 | 15.32 |
AT1G16610 | SR45 | 精氨酸/丝氨酸丰富45 Arginine/serine-rich 45 | 0.06 | 2.02E-16 | 1.89 |
AT5G51660 | CPSF160 | 切割与多聚腺苷酸化特异性因子160 Cleavage and polyadenylation specificity factor 160 | 0.01 | 2.02E-16 | 0.00 |
AT5G47010 | LBA1 | RNA解旋酶 RNA helicase | 0.01 | 2.02E-16 | 0.00 |
RNA降解RNA degradation | |||||
AT5G61580 | PFK4 | 磷酸果糖激酶4 Phosphofructokinase 4 | 100.00 | 2.02E-16 | 0.00 |
AT5G02270 | ABCI20 | 非本征ABC蛋白9 Non-intrinsic ABC protein 9 | 0.46 | 2.02E-16 | 4.33 |
AT5G35430 | NOT10 | 四肽重复序列类超家族蛋白 Tetratricopeptide repeat(TPR)-like superfamily protein | 0.04 | 2.02E-16 | 0.36 |
AT4G32840 | PFK6 | 磷酸果糖激酶6 Phosphofructokinase 6 | 0.01 | 2.02E-16 | 0.00 |
AT3G20800 | NOT9A | 细胞分化,Rcd1类蛋白 Cell differentiation,Rcd1-like protein | 0.01 | 8.72E-03 | 0.00 |
苯丙素的生物合成Phenylpropanoid biosynthesis | |||||
AT2G18980 | PRX16 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 100.00 | 2.02E-16 | 0.00 |
AT5G66390 | PRX72 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 2.07 | 2.02E-02 | 41.96 |
AT1G66270 | BGLU21 | 糖基水解酶超家族蛋白,β-葡萄糖苷酶 Glycosyl hydrolase superfamily protein,β-glucosidase | 0.63 | 4.18E-02 | 1.71 |
AT1G66280 | BGLU22 | 糖基水解酶超家族蛋白,β-葡萄糖苷酶 Glycosyl hydrolase superfamily protein,β-glucosidase | 0.44 | 3.47E-06 | 7.12 |
AT5G64120 | PRX71 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 0.30 | 1.57E-11 | 1.14 |
AT2G38390 | PRX23 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 0.14 | 3.52E-14 | 0.75 |
AT4G33420 | PRX47 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 0.11 | 1.57E-11 | 9.98 |
表1 显著富集的KEGG通路中的差异表达蛋白
Table 1 Differentially expressed proteins in the significantly enriched KEGG pathways
拟南芥基因号 AGI locus ID | 蛋白质名称 Protein name | 描述 Description | 丰度比Abundance ratio | 丰度比的调整P值 Abundance ratio adj. P value | 丰度比变异性 Abundance ratio variability/% |
---|---|---|---|---|---|
核糖体Ribosome | |||||
AT3G49080 | RPS9M | 核糖体蛋白S9 M Ribosomal protein S9 M | 100.00 | 2.02E-16 | 0.00 |
AT2G21580 | RPS25B | 核糖体蛋白S25家族蛋白 Ribosomal protein S25 family protein | 11.39 | 2.02E-16 | 642.26 |
AT2G19740 | RPL31A | 核糖体蛋白L31e家族蛋白 Ribosomal protein L31e family protein | 0.63 | 3.50E-02 | 7.21 |
AT5G56670 | RPS30C | 核糖体蛋白S30家族蛋白 Ribosomal protein S30 family protein | 0.59 | 4.08E-02 | 3.33 |
AT3G46040 | RPS15aD | 核糖体蛋白S15a D Ribosomal protein S15a D | 0.58 | 2.65E-02 | 1.03 |
AT5G16130 | RPS7C | 核糖体蛋白S7e家族蛋白 Ribosomal protein S7e family protein | 0.57 | 8.83E-04 | 2.09 |
AT1G04270 | RPS15A | 核糖体蛋白S15 Ribosomal protein S15 | 0.53 | 6.16E-03 | 14.83 |
AT5G18380 | RPS16C | 核糖体蛋白S5结构域2类似超家族蛋白Ribosomal protein S5 domain 2-like superfamily protein | 0.51 | 1.27E-04 | 8.10 |
AT5G23900 | RPL13D | 核糖体蛋白L13e家族蛋白 Ribosomal protein L13e family protein | 0.49 | 1.49E-04 | 4.12 |
AT2G27720 | RPP2A | 60S酸性核糖体蛋白家族 60S acidic ribosomal protein family | 0.43 | 1.14E-05 | 1.49 |
AT3G28900 | RPL34C | 核糖体蛋白L34e超家族蛋白质 Ribosomal protein L34e superfamily protein | 0.33 | 1.77E-04 | 2.55 |
AT1G01100 | RPP1A | 60S酸性核糖体蛋白家族 60S acidic ribosomal protein family | 0.01 | 2.02E-16 | 0.00 |
光合作用Photosynthesis | |||||
ATCG00020 | PSBA | 光系统II反应中心蛋白D1 Phot-osystem II reaction center protein D1 | 1.75 | 6.17E-04 | 18.27 |
ATCG00270 | PSBD | P光系统II反应中心蛋白D2 Pho-tosystem II reaction center protein D2 | 1.69 | 1.53E-03 | 16.06 |
ATCG00580 | PSBE | 光系统II反应中心蛋白V Phot-osystem II reaction center protein V | 0.62 | 3.90E-02 | 7.74 |
ATCG00470 | ATPE | ATP合酶ε亚基 ATP synthase epsilon subunit | 0.58 | 1.20E-02 | 4.17 |
AT1G10960 | FD1 | 铁氧还原蛋白1 Ferredoxin 1 | 0.01 | 2.02E-16 | 0.00 |
mRNA监视通路mRNA surveillance pathway | |||||
AT1G13320 | PP2AA3 | 蛋白磷酸酶2A亚基A3 Protein phosphatase 2A subunit A3 | 100.00 | 2.02E-16 | 0.00 |
AT1G02140 | MAGO | Mago nashi家族蛋白 Mago nashi family protein | 2.23 | 1.48E-05 | 20.68 |
AT1G17720 | ATB BETA | 蛋白磷酸酶2A,调控亚基PR55 Protein phosphatase 2A,regulatory subunit PR55 | 0.13 | 1.44E-12 | 15.32 |
AT1G16610 | SR45 | 精氨酸/丝氨酸丰富45 Arginine/serine-rich 45 | 0.06 | 2.02E-16 | 1.89 |
AT5G51660 | CPSF160 | 切割与多聚腺苷酸化特异性因子160 Cleavage and polyadenylation specificity factor 160 | 0.01 | 2.02E-16 | 0.00 |
AT5G47010 | LBA1 | RNA解旋酶 RNA helicase | 0.01 | 2.02E-16 | 0.00 |
RNA降解RNA degradation | |||||
AT5G61580 | PFK4 | 磷酸果糖激酶4 Phosphofructokinase 4 | 100.00 | 2.02E-16 | 0.00 |
AT5G02270 | ABCI20 | 非本征ABC蛋白9 Non-intrinsic ABC protein 9 | 0.46 | 2.02E-16 | 4.33 |
AT5G35430 | NOT10 | 四肽重复序列类超家族蛋白 Tetratricopeptide repeat(TPR)-like superfamily protein | 0.04 | 2.02E-16 | 0.36 |
AT4G32840 | PFK6 | 磷酸果糖激酶6 Phosphofructokinase 6 | 0.01 | 2.02E-16 | 0.00 |
AT3G20800 | NOT9A | 细胞分化,Rcd1类蛋白 Cell differentiation,Rcd1-like protein | 0.01 | 8.72E-03 | 0.00 |
苯丙素的生物合成Phenylpropanoid biosynthesis | |||||
AT2G18980 | PRX16 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 100.00 | 2.02E-16 | 0.00 |
AT5G66390 | PRX72 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 2.07 | 2.02E-02 | 41.96 |
AT1G66270 | BGLU21 | 糖基水解酶超家族蛋白,β-葡萄糖苷酶 Glycosyl hydrolase superfamily protein,β-glucosidase | 0.63 | 4.18E-02 | 1.71 |
AT1G66280 | BGLU22 | 糖基水解酶超家族蛋白,β-葡萄糖苷酶 Glycosyl hydrolase superfamily protein,β-glucosidase | 0.44 | 3.47E-06 | 7.12 |
AT5G64120 | PRX71 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 0.30 | 1.57E-11 | 1.14 |
AT2G38390 | PRX23 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 0.14 | 3.52E-14 | 0.75 |
AT4G33420 | PRX47 | 过氧化物酶超家族蛋白 Peroxidase superfamily protein | 0.11 | 1.57E-11 | 9.98 |
图5 WT和rpp1a-2突变体幼苗差异蛋白的KEGG富集分析
Fig. 5 KEGG enrichment analysis of differentially expr-essed proteins identified in the WT and rpp1a-2 mutant seedlings
图6 差异蛋白的蛋白质互作网络 圆圈大小与互作关系的数目成正比
Fig. 6 Protein-protein interaction network of differentially expressed proteins Size of the circle is proportional to the number of interaction relationships
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