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Journal of Zhejiang University (Agriculture and Life Sciences)  2021, Vol. 47 Issue (3): 325-334    DOI: 10.3785/j.issn.1008-9209.2020.09.141
Horticulture     
Bioinformatics of 1-aminocyclopropane-1-carboxylic acid synthase gene from eggplant and its expression analysis in response to adversity stresses
Faxiang WAN(),Lianzhen WANG,Jun GAO
School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, Jiangsu, China
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Abstract  

Based on the early transcriptome data of eggplant under cold stress, the 1-aminocyclopropane-1-carboxylic acid (ACC) synthase gene SmACS was selected out. It was found that the encoded amino acid sequence of SmACS had the highest homology with soybean ACS protein, and included seven conserved domains unique to ACC synthase and 11 invariant amino acid residues. The SmACS gene was located on the chromosome 8, and the full length of this gene was 3 550 bp, whose length of coding sequence (CDS) region was 1 437 bp. It contained three introns and four exons, which belonged to a typical ACS gene structure. The SmACS protein consisted of 478 amino acids, with a molecular mass of 54.03 kDa, isoelectric point of 6.48 and hydrophilic index of -0.206. It was an unstable non-secreted hydrophilic protein located in the cytoplasm. The main components of SmACS protein were α-helix and random coils. It had a conserved Aminotran_1_2 domain and contained 39 phosphorylation sites, of which serine and threonine were the main ones. The SmACS protein mainly interacted with ACC oxidase. The promoter of SmACS gene contained Cis-acting elements related to abscisic acid, ethylene, cold stress, salicylic acid and wound responses. The results of real-time fluorescent quantitative polymerase chain reaction (qRT-PCR) confirmed that the expression of SmACS gene was induced by cold, heat, drought and salt stresses, among which cold stress was the most significant. The above results lay theoretical basis for functional identification of SmACS gene from eggplant.



Key wordseggplant      1-aminocyclopropane-1-carboxylic acid synthase gene      bioinformatics      expression analysis     
Received: 14 September 2020      Published: 25 June 2021
CLC:  S 641.1  
Corresponding Authors: Faxiang WAN     E-mail: wanfaxiang@hyit.edu.cn
Cite this article:

Faxiang WAN,Lianzhen WANG,Jun GAO. Bioinformatics of 1-aminocyclopropane-1-carboxylic acid synthase gene from eggplant and its expression analysis in response to adversity stresses. Journal of Zhejiang University (Agriculture and Life Sciences), 2021, 47(3): 325-334.

URL:

http://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2020.09.141     OR     http://www.zjujournals.com/agr/Y2021/V47/I3/325


茄子1-氨基环丙烷-1-羧酸合成酶基因的生物信息学及其响应逆境胁迫的表达分析

基于课题组前期得到的茄子低温转录组数据,筛选到1个1-氨基环丙烷-1-羧酸(1-aminocyclopropane-1-carboxylic acid, ACC)合成酶基因SmACS。研究发现,SmACS编码的氨基酸序列与大豆ACS的同源性最高,并且含有ACC合成酶特有的7个保守结构域和11个不变的氨基酸残基。该SmACS基因位于第8号染色体上,全长 3 550 bp,编码序列长1 437 bp,含3个内含子和4个外显子,属典型的ACS基因结构。其编码的蛋白质由478个氨基酸组成,分子质量为54.03 kDa,等电点为6.48,亲水系数为-0.206,是一种定位于细胞质的不稳定的非分泌型亲水蛋白;该蛋白的主要构成元件为α-螺旋和无规则卷曲,具有保守的Aminotran_1_2结构域,含有39个磷酸化位点,其中以丝氨酸和苏氨酸为主。SmACS蛋白主要与ACC氧化酶等发生相互作用。该基因启动子中含有脱落酸、乙烯、冷胁迫、水杨酸及伤口响应等有关的顺式作用元件。实时荧光定量聚合酶链式反应(real-time fluorescent quantitative polymerase chain reaction, qRT-PCR)结果证实,SmACS基因受低温、高温、干旱和盐诱导而上调表达,其中尤以低温胁迫诱导效果最为显著。上述结果可为进一步研究茄子SmACS基因的功能奠定理论基础。


关键词: 茄子,  1-氨基环丙烷-1-羧酸合成酶基因,  生物信息学,  表达分析 

基因名称

Gene name

引物序列(5′→3′)

Primer sequence (5′→3′)

SmACSF: TGTCTTCTCCTATGGTCCAAGC
R: TGGATGTATCCATGAACGCCT
APRTF: GAGATGCATGTAGGTGCTGTGCAA
R: GGCCCTTCAATTCTGGCAACTCAA
Table 1 Primer sequences
Fig. 1 Phylogenetic tree of the amino acid sequence of SmACS protein from eggplant and homologous sequences from other species
Fig. 2 Results of multiple alignment among SmACS protein from eggplant and ACS proteins from other speciesRed arrows indicate the conserved amino acids in transaminase; the conserved glutamate residues marked by the purple dots are related to the substrate specificity; and the seven conserved domains of the ACS isozyme are marked by the red boxes (Box1-Box7).
Fig. 3 Conserved motif analysis of SmACS protein from eggplant
Fig. 4 Structure analysis of SmACS gene from eggplant
Fig. 5 Predicted results of secondary structure of SmACS protein from eggplantA. Histogram of secondary structure of SmACS protein; B. Linear change curve of SmACS protein. Blue: α-helix; Red: Extended chain; Green: β-turn; Purple: Random curl.
Fig. 6 Predicted result of tertiary structure of SmACS protein from eggplant
Fig. 7 Conserved domain of SmACS protein from eggplant
Fig. 8 Phosphorylation sites of SmACS protein from eggplant
Fig. 9 Interaction network of ACS1A protein

位点名称

Site name

数量

Number

功能

Function

ABRE1脱落酸响应顺式作用元件 Cis-acting element involved in the abscisic acid response
circadian1光周期响应有关的顺式作用元件 Cis-acting element related to photoperiod response
ERE8乙烯响应元件 Ethylene-responsive element
MRE1MYB光反应结合位点 MYB photoreactive binding site
MYC5

脱落酸响应和冷胁迫中涉及的顺式作用元件

Cis-acting elements involved in abscisic acid response and cold stress

O2-site2玉米醇溶蛋白代谢有关的顺式作用元件 Cis-acting elements related to zein metabolism
TCA1水杨酸响应顺式作用元件 Cis-acting element involved in salicylic acid response
WUN-motif1伤口响应元件 Wound-responsive element
Table 2 Main Cis-acting elements in the promoter region of SmACS gene
Fig. 10 Expression analysis of SmACS gene from eggplant in response to adversity stresses
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