基因加倍对棉花线粒体atpA基因RNA编辑率的影响

doi:10.19586/j.2095-2341.2022.0041

生物技术进展 ›› 2022, Vol. 12 ›› Issue (5): 737-745.DOI: 10.19586/j.2095-2341.2022.0041

基因加倍对棉花线粒体atpA基因RNA编辑率的影响

张晓¹^,²(), 李才华¹, 王婧¹, 张兰兰¹, 牟晓雨¹, 王昕玥¹, 甘刘美¹, 周鹏展¹, 张锐²()

^1.长春理工大学生命科学技术学院，长春 130022
^2.中国农业科学院生物技术研究所，北京 100081

收稿日期:2022-03-18 接受日期:2022-04-22 出版日期:2022-09-25 发布日期:2022-09-30
通讯作者: 张锐
作者简介:张晓 E-mail: enerrgy@126.com；
基金资助:
国家自然科学基金青年基金项目(31200944);国家自然科学基金项目(31771850)

Impact of Gene Duplication on RNA Editing Rates of Mitochondrial atpA Gene in Cotton （Gossypium hirsutum L.）

Xiao ZHANG¹^,²(), Caihua LI¹, Jing WANG¹, Lanlan ZHANG¹, Xiaoyu MOU¹, Xinyue WANG¹, Liumei GAN¹, Pengzhan ZHOU¹, Rui ZHANG²()

^1.School of life Science and Technology，Changchun University of Science and Technology，Changchun 130022，China
^2.Biotechnology Research Institute，Chinese Academy of Agricultural Sciences，Beijing 100081，China

Received:2022-03-18 Accepted:2022-04-22 Online:2022-09-25 Published:2022-09-30
Contact: Rui ZHANG

摘要/Abstract

摘要：

植物线粒体基因组中存在RNA编辑（C-U）现象，且有完全编辑和部分编辑之分。棉花细胞质雄性不育（cytoplasmic male sterile，CMS）系和保持系线粒体基因组中atpA基因各有两个拷贝，存在基因加倍现象，但atpA基因加倍对其RNA编辑率的影响尚不清楚。通过Southern blot、染色体步移技术确定出该基因每个拷贝具体的DNA序列，发现一个拷贝是完整的，一个拷贝是截短的。用RT-PCR、环化RT-PCR方法扩增出每个拷贝相应的cDNA，结果表明：棉花CMS系和保持系atpA基因完整拷贝和截短型拷贝都转录。完整拷贝、截短型拷贝中分别存在6、4个RNA编辑位点。完整拷贝6个RNA编辑位点在保持系中的编辑率都是100%；在CMS系中编辑率分别是100%、85%、100%、92%、100%、100%。截短型拷贝4个位点在保持系中的编辑率分别是55%、37%、55%、27%；在CMS系中编辑率分别是100%、90%、100%、100%。据此推测截短型拷贝在保持系中承受选择压较小，很可能已失去功能；而在CMS系中仍承受较大选择压，很可能具有新的功能。

关键词: 棉花, 线粒体基因组, atpA, 基因加倍, RNA编辑

Abstract:

C-U RNA editing exists in plant mitochondrial genome， and it can be divided into complete editing and partial editing. There are two copies of atpA gene in the mitochondrial genomes of cytoplasmic male sterile （CMS） line and maintainer line of cotton， indicating gene duplication. However， the impact of atpA gene duplication on RNA editing rate is still unclear. In this study， the specific sequences of each copy of atpA gene were cloned by Southern blot and choromosomal walking methods， showing that one copy was intact and the other copy was truncated in each line. The corresponding cDNAs were further amplified with RT-PCR and circular RT-PCR methods. The sequencing results showed that both the intact copy and the truncated copy of atpA gene in CMS and maintainer line were transcribed. There were 6 RNA editing sites in the intact atpA copies， and 4 RNA editing sites in the truncated copies. The RNA editing rates of the 6 sites of intact copy in maintainer line were 100%； while the RNA editing rates of the 6 sites of intact copy in CMS line were 100%， 85%， 100%， 92%， 100%， 100%， respectively. The editing rates of the 4 sites of the truncated copy in maintainer line were 55%， 37%， 55%， 27%， respectively； while the RNA editing rates of the 4 sites of the truncated copy in CMS line were 100%， 90%， 100%， 100%， respectively. It was speculated that the truncated copy in the maintaining line bears less selective pressure and may have lost its function； while the truncated atpA copy in the CMS line was still under high selective pressure and was likely to have new functions.

Key words: cotton, mitochondrial genome, atpA, gene duplication, RNA editing

中图分类号:

S562

张晓, 李才华, 王婧, 张兰兰, 牟晓雨, 王昕玥, 甘刘美, 周鹏展, 张锐. 基因加倍对棉花线粒体atpA基因RNA编辑率的影响[J]. 生物技术进展, 2022, 12(5): 737-745.

Xiao ZHANG, Caihua LI, Jing WANG, Lanlan ZHANG, Xiaoyu MOU, Xinyue WANG, Liumei GAN, Pengzhan ZHOU, Rui ZHANG. Impact of Gene Duplication on RNA Editing Rates of Mitochondrial atpA Gene in Cotton （Gossypium hirsutum L.）[J]. Current Biotechnology, 2022, 12(5): 737-745.

图/表 8

表1 研究使用的引物

Table 1 Primers used in this study

引物名称	引物序列（5'→3'）	长度/nt	T_m/℃	用途
atpAF	5'-ATTTTCAAGTGGATGAGATCGG-3'	22	59	Southern blot
atpAR	5'-GATCACAGAATCCATTGACAGC-3'	22	61	Southern blot
atpAIF	5'-CTGGAATTGGCACAATATCGCGAAGTGG-3'	28	65	IPCRcRT-PCR
atpAIR	5'-TCAACCATTTCCCCAGCTTGAATCTCGT-3'	28	63	IPCRcRT-PCR
atpA-F	5'-TTACCAGCTCGGGGATCTAATC-3'	20	60	RT-PCR
1R	5'-CACTCGCTCGCCTTCGGGTGAGG-3'	23	69	RT-PCR
N2R	5'-ATCGAGTTAGAGATCGGGTTGCAGG-3'	25	64	RT-PCR
S2R	5'-ATGGAAATCCTCTTTAGCAGCCTGC-3'	25	62	RT-PCR

图1 陆地棉细胞质雄性不育系、保持系总DNA的Southern blot分析注：S—棉花CMS不育系；N—保持系。（N）atpA-1和（S）atpA-1含有完整的atpA基因编码序列（1 524 bp），并具有相似的3'延伸区，但是在atpA终止密码子下游161~212 bp区域，存在一个SSR位点。该位点在保持系中是（TAA）7（TA）6，在CMS中是（TAA）3（TA）2。

Fig. 1 Southern blot analysis of total DNAs of CMS, maintainer line of Gossypium hirsutum L.

图2 棉花CMS和保持系中atpA基因Hind Ⅲ限制性片段

Fig. 2 HindⅢrestriction fragments of atpA gene in CMS and maintainer line of cotton.

图3 棉花CMS和保持系中atpA基因的RT-PCR分析注：M—DNA Marker； S—棉花CMS不育系； N—保持系。

Fig. 3 RT-PCR analysis of atpA gene in CMS and maintainer line of cotton

表2 棉花CMS系全长和截短型atpA基因转录起始位点和终止位点情况

Table 2 Start and termination sites of transcripts of intact and truncated atpA gene in CMS line of cotton

拷贝类型		转录起始位点					转录终止位点
全长拷贝	位点/bp	-81	-82	-63	-60	-59	+200	+202	+210
全长拷贝	数目	10	3	2	1	1	10	6	1
截短拷贝	位点/bp	-81	-80	-69	-77		+249	+248	+250	+247	+246	+224	+144
截短拷贝	数目	10	5	3	1		10	4	1	1	1	1	1

图4 棉花CMS和保持系atpA基因Northern blot分析注：S—棉花CMS不育系； N—保持系。

Fig. 4 Northern blot analysis of atpA gene in CMS and maintainer line of cotton

表3 棉花atpA编辑位点与其他植物的比较

Table 3 Comparison of cotton atpA editing sites with those of other plants

编辑位点（氨基酸）	10	13	324	347	355	393	406	431	472	495	497	500
提莫菲维小麦（T. timopheevi）	L-L	L	S-L	—	—	S-L	—	P-L	L	—	P-L	S-F
普通小麦（T. aestivum）	L-L	L	S-L	—	—	S-L	—	P-L	L	—	P-L	S-F
黑小麦（Triticale）	L-L	L	S-L	—	—	S-L	—	P-L	L	—	P-L	S-F
月见草（Oenothera）	L	L-L	S-L	—	—	L	—	L	P-L	—	P-L	F
甜菜（Beta vulgaris L.）	L	L	L	—	—	P-L	—	P-L	P-L	—	L	F
棉花(Gossypium hirsutum L.)	L	L	L	P-S	S-L	L	L-F	P-L	P-L	P-L	T	K

表4 棉花CMS系(S)和保持系(N)atpA基因完整拷贝和截短型拷贝的RNA编辑率比较

Table 4 Comparison of RNA editing rates of intact and truncated copies of atpA gene in CMS line(S) and maintainer line(N) of cotton

编辑位点	1 039 bp	1 064 bp	1 216 bp	1 292 bp	1 415 bp	1 484 bp
氨基酸的变化	P-S	S-L	L-F	P-L	P-L	P-L
（N）atpA-1	100%	100%	100%	100%	100%	100%
（S）atpA-1	100%	85%	100%	92%	100%	100%
（N）atpA-2	55%	37%	55%	27%	—	—
（S）atpA-2	100%	90%	100%	100%	—	—

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基因加倍对棉花线粒体atpA基因RNA编辑率的影响

Impact of Gene Duplication on RNA Editing Rates of Mitochondrial atpA Gene in Cotton （Gossypium hirsutum L.）

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