拟南芥RPP1A参与幼苗生长的蛋白质组学分析

doi:10.13560/j.cnki.biotech.bull.1985.2021-0542

摘要/Abstract

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。

关键词: 拟南芥, 核糖体蛋白, 幼苗生长, 蛋白质组, 刺激反应, 光合作用

Abstract:

Ribosomal proteins are not only involved in protein synthesis but also regulate plant growth and development. Arabidopsis thaliana ribosomal phosphoprotein P1（RPP1）family RPP1A deletion mutant rpp1a was used to investigate the effect of RPP1A deletion on the protein profile of seedlings and to reveal the mechanism of its involvement in regulation of seedling growth. Phenotypic analysis revealed that the RPP1A deletion resulted in significant increases in biomass,total leaf surface area,and petiole length of the seedlings compared with wild-type（WT）. The label-free proteomic analysis revealed that a total of 280 differentially expressed proteins were identified in the mutant rpp1a-2 compared with the WT,with 98 proteins significantly up-regulated and 182 proteins significantly down-regulated. Differentially expressed proteins were mainly involved in cellular process,metabolic process,response to stimulus,cellular component organization or biogenesis,and oxidation-reduction process,and were significantly enriched in the metabolic pathways of ribosome,photosynthesis,mRNA surveillance pathway,RNA degradation and phenylpropanoid biosynthesis. The A. thaliana rpp1a-2 mutant promotes plant growth by inhibiting the stimulus-response and enhancing photosynthesis.

Key words: Arabidopsis thaliana, ribosomal proteins, seedling growth, proteomics, stimulus response, photosynthesis

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/表 7

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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

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