大白菜BrSPS1Fb基因剪接受体位点变异及其对剪接的影响

doi:10.3969/j.issn.1004-1524.2021.11.09

浙江农业学报 ›› 2021, Vol. 33 ›› Issue (11): 2068-2074.DOI: 10.3969/j.issn.1004-1524.2021.11.09

大白菜BrSPS1Fb基因剪接受体位点变异及其对剪接的影响

陶鹏(), 岳智臣, 赵彦婷, 雷娟利, 李必元^*()

浙江省农业科学院蔬菜研究所,浙江杭州 310021

收稿日期:2020-10-28 出版日期:2021-11-25 发布日期:2021-11-26
通讯作者: 李必元
作者简介:*李必元,E-mail: 16061944@qq.com
陶鹏(1984—),男,江西南昌人,博士,副研究员,主要从事十字花科蔬菜育种与分子生物学研究。E-mail: taopeng- 84@163.com
基金资助:
浙江省自然科学基金(LY21C150006);浙江省农业新品种选育重大科技专项(2017C02065);宁波市农业重大科技专项(2016C11002)

Variation of acceptor splicing site of BrSPS1Fb of Chinese cabbage and its effect on splicing

TAO Peng(), YUE Zhichen, ZHAO Yanting, LEI Juanli, LI Biyuan^*()

Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China

Received:2020-10-28 Online:2021-11-25 Published:2021-11-26
Contact: LI Biyuan

摘要/Abstract

摘要：

为研究剪接受体位点变异对剪接方式与效率的影响,对大白菜材料He2进行重测序,发现BrSPS1Fb-He2第6个内含子(I6)的剪接受体位点由AG突变为AC。对大白菜材料He2花瓣进行转录组测序并分析BrSPS1Fb-He2 read数据,结果显示,BrSPS1Fb-He2在pre-mRNA加工过程中发生了选择性剪接。BrSPS1Fb-He2可选择3个位置(A1、A2和A3)作为受体进行剪接,产生3种剪接异构体(S1、S2和S3),或者保留I6整个内含子,形成S4剪接异构体。大白菜BrSPS1Fb-He2的成熟mRNA中保留部分I6(S1和S2)或全部I6(S4),或者缺失部分E7外显子序列(S3)。综上,BrSPS1Fb剪接受体位点的单核苷酸多态性(single nucleotide polymorphisms,SNP)变异对其转录后剪接产生了显著影响。

关键词: 大白菜, 单核苷酸多态性(SNP), 剪接受体位点, SPS1F, 选择性剪接

Abstract:

To investigate the effect of variation of acceptor splicing site on splicing pattern and efficiency, the inbred line “He2” of Chinese cabbage was re-sequenced, and the result indicated that acceptor splicing site of the sixth intron (I6) of BrSPS1Fb-He2 was changed from AG to AC. Through analysis of BrSPS1Fb-He2 read data from transcriptome sequencing library of petals of the “He2” inbred line, it was found that alternative splicing occurred during pre-mRNA processing of BrSPS1Fb-He2. Three sites (A1, A2 and A3) of BrSPS1Fb-He2 could be selected as splicing acceptor during pre-mRNA splicing, resulting correspondingly in the three spliced isoforms (S1, S2 and S3), or the entire I6 was retained to form S4 spliced isoform. Partial I6 was retained in mature mRNA of S1 and S2, the whole I6 in S4, partial E7 was deleted in S3. This study indicated that single nucleotide polymorphisms (SNP) variation of acceptor splicing site had a significant impact on post transcriptional splicing of BrSPS1Fb.

Key words: Chinese cabbage, single nucleotide polymorphisms (SNP), acceptor splicing site, SPS1F, alternative splicing

中图分类号:

S634.1

陶鹏, 岳智臣, 赵彦婷, 雷娟利, 李必元. 大白菜BrSPS1Fb基因剪接受体位点变异及其对剪接的影响[J]. 浙江农业学报, 2021, 33(11): 2068-2074.

TAO Peng, YUE Zhichen, ZHAO Yanting, LEI Juanli, LI Biyuan. Variation of acceptor splicing site of BrSPS1Fb of Chinese cabbage and its effect on splicing[J]. Acta Agriculturae Zhejiangensis, 2021, 33(11): 2068-2074.

图/表 5

表1 所使用的检索序列

Table 1 Retrieval sequences

名称 Name	检索对象 Retrieval object	序列(5'-3') Sequence (5'-3')
PA	BrSPS1Fa	CGAGATCCACCAATATGGGCTGAG
PB	BrSPS1Fb	CGGGATCCACCAATATGGGCTGAG
PA1	BrSPS1Fa-S1	CGAGATCCACCAATATGGGCTGAGCTGT
PA2	BrSPS1Fa-S2	CGAGATCCACCAATATGGGCTGAGGTGA
PA3	BrSPS1Fa-S3	CGAGATCCACCAATATGGGCTGAGCCTA
PA4	BrSPS1Fa-S4	CGAGATCCACCAATATGGGCTGAGGTTC
PA5	BrSPS1Fa-S5	CGAGATCCACCAATATGGGCTGAGATAA
PB1	BrSPS1Fb-S1	CGGGATCCACCAATATGGGCTGAGAGCT
PB2	BrSPS1Fb-S2	CGGGATCCACCAATATGGGCTGAGGTGA
PB3	BrSPS1Fb-S3	CGGGATCCACCAATATGGGCTGAGCCTA
PB4	BrSPS1Fb-S4	CGGGATCCACCAATATGGGCTGAGGTTC
PB5	BrSPS1Fb-S5	CGGGATCCACCAATATGGGCTGAGATAA

图1 大白菜BrSPS1Fb-Chiifu401内含子-外显子结构与大白菜He2 BrSPS1Fb剪接受体位点的SNP变异

Fig.1 Intron-exon structure of BrSPS1Fb-Chiifu401 of Chinese cabbage and SNP variation of acceptor splicing site of BrSPS1Fb in the inbred line He2 of Chinese cabbage

图2 BrSPS1Fb-He2基因的剪接异构体与剪接位点位置 A,大白菜He2的BrSPS1Fb-He2基因4种剪接异构体及其相对应的剪接供体位点和剪接受体位点。B,BrSPS1Fb-He2基因的剪接供体位点和剪接受体位点的位置。黑色背景和灰色背景分别代表外显子和内含子。

Fig.2 Splicing isoforms and location of splicing sites of BrSPS1Fb-He2 A, Four splicing isoforms of BrSPS1Fb-He2 of Chinese cabbage He2 and their corresponding donor splicing sites and acceptor splicing sites. B, Location of donor splicing sites and acceptor splicing sites of the BrSPS1Fb-He2 gene. Black and gray background represented the sequence of exon and intron, respectively.

图3 大白菜BrSPS1Fa和BrSPS1Fb基因的剪接异构体的比例

Fig.3 Proportion of splicing isoforms of BrSPS1Fa and BrSPS1Fb of Chinese cabbage

图4 大白菜BrSPS1Fb-He2的蛋白产物与BrSPS1Fb-Chiifu401的氨基酸序列比对

Fig.4 Alignment of amino acid sequences of protein products of BrSPS1Fb-He2 of Chinese cabbage and BrSPS1Fb-Chiifu401 protein

参考文献 19

[1]	SWARUP R, CRESPI M, BENNETT M J. One gene, many proteins: mapping cell-specific alternative splicing in plants[J]. Developmental Cell, 2016, 39(4):383-385. DOI URL
[2]	REDDY A S N, MARQUEZ Y, KALYNA M, et al. Complexity of the alternative splicing landscape in plants[J]. The Plant Cell, 2013, 25(10):3657-3683. DOI URL
[3]	逄洪波, 解元坤, 李嘉琦, 等. 可变剪切在动植物中的研究进展[J]. 基因组学与应用生物学, 2020, 39(4):1595-1600.
	PANG H B, XIE Y K, LI J Q, et al. Research progress of alternative splicing in plants and animals[J]. Genomics and Applied Biology, 2020, 39(4):1595-1600.(in Chinese with English abstract)
[4]	宋凝曦, 张晓敬, 陆佳岚, 等. 可变剪接在植物响应胁迫中的作用[J]. 植物生理学报, 2020, 56(6):1201-1211.
	SONG N X, ZHANG X J, LU J L, et al. Function of alternative splicing in plant response to biotic and abiotic stress[J]. Plant Physiology Journal, 2020, 56(6):1201-1211.(in Chinese with English abstract)
[5]	陈伶莉, 胡雪峰. 内含子的特异性识别与选择性剪切[J]. 生物学通报, 2018, 53(12):12-15.
	CHEN L L, HU X F. Specific recognition and selective cleavage of introns[J]. Bulletin of Biology, 2018, 53(12):12-15.(in Chinese)
[6]	YUAN Y X, WU J, SUN R F, et al. A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time[J]. Journal of Experimental Botany, 2009, 60(4):1299-1308. DOI URL
[7]	MALONEY V J, PARK J Y, UNDA F, et al. Sucrose phosphate synthase and sucrose phosphate phosphatase interact in planta and promote plant growth and biomass accumulation[J]. Journal of Experimental Botany, 2015, 66(14):4383-4394. DOI URL
[8]	TAO P, WANG J B. Characterization of the variable 3'UTR and expression of the two intron-containing KIN transcripts from Capsella bursa-pastoris[J]. Gene, 2012, 507(2):99-105. DOI URL
[9]	TAO P, PENG L F, HUANG X J, et al. Comparative analysis of the variable 3'UTR and gene expression of the KIN and KIN-homologous LEA genes in Capsella bursa-pastoris[J]. Plant Cell Reports, 2012, 31(10):1769-1777. DOI URL
[10]	TAO P, HUANG X Y, LI B Y, et al. Comparative analysis of alternative splicing, alternative polyadenylation and the expression of the two KIN genes from cytoplasmic male sterility cabbage (Brassica oleracea L. var. capitata L.)[J]. Molecular Genetics and Genomics, 2014, 289(3):361-372. DOI URL
[11]	陶鹏, 钟新民, 李必元, 等. CMS结球甘蓝剪接异构体BoKIN1-2的鉴定及其表达研究[J]. 核农学报, 2015, 29(11):2077-2083.
	TAO P, ZHONG X M, LI B Y, et al. Analysis of identification and the expression of splicing isoform BoKIN1-2 from CMS cabbage (Brassica oleracea L. var. capitata L.)[J]. Journal of Nuclear Agricultural Sciences, 2015, 29(11):2077-2083.(in Chinese with English abstract)
[12]	REDDY A S N, SHAD ALI G. Plant serine/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses[J]. Wiley Interdisciplinary Reviews: RNA, 2011, 2(6):875-889.
[13]	曲瑞莲, 吴春霞, 冯献忠. mRNA选择性剪切在植物发育中的作用[J]. 植物生理学报, 2014, 50(6):717-724.
	QU R L, WU C X, FENG X Z. Function of mRNA alternative splicing in plant development[J]. Plant Physiology Journal, 2014, 50(6):717-724.(in Chinese with English abstract)
[14]	BARTYS N, KIERZEK R, LISOWIEC-WACHNICKA J. The regulation properties of RNA secondary structure in alternative splicing[J]. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2019, 1862(11/12):194401.
[15]	IRIMIA M, BLENCOWE B J. Alternative splicing: decoding an expansive regulatory layer[J]. Current Opinion in Cell Biology, 2012, 24(3):323-332. DOI URL
[16]	HAN H, BRAUNSCHWEIG U, GONATOPOULOS-POURNATZIS T, et al. Multilayered control of alternative splicing regulatory networks by transcription factors[J]. Molecular Cell, 2017, 65(3): 539-553. e7. DOI URL
[17]	OTTENS F, GEHRING N H. Physiological and pathophysiological role of nonsense-mediated mRNA decay[J]. Pflügers Archiv-European Journal of Physiology, 2016, 468(6):1013-1028. DOI URL
[18]	SUN J D, ZHANG J S, LARUE C T, et al. Decrease in leaf sucrose synjournal leads to increased leaf starch turnover and decreased RuBP regeneration-limited photosynjournal but not rubisco-limited photosynjournal in Arabidopsis null mutants of SPSA1[J]. Plant, Cell & Environment, 2011, 34(4):592-604.
[19]	张古文, 胡齐赞, 徐盛春, 等. 菜用大豆籽粒发育过程中蔗糖积累及相关酶活性的研究[J]. 浙江农业学报, 2012, 24(6):1015-1020.
	ZHANG G W, HU Q Z, XU S C, et al. Study on sucrose accumulation and enzyme activities involved in sucrose metabolism in developing seeds of vegetable soybean[J]. Acta Agriculturae Zhejiangensis, 2012, 24(6):1015-1020.(in Chinese with English abstract)

大白菜BrSPS1Fb基因剪接受体位点变异及其对剪接的影响

Variation of acceptor splicing site of BrSPS1Fb of Chinese cabbage and its effect on splicing

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