Identification of RcGeBP transcription factor and cloning and expression analysis of RcGeBP2 gene in castor

doi:10.3969/j.issn.1004-1524.20230833

Acta Agriculturae Zhejiangensis ›› 2024, Vol. 36 ›› Issue (8): 1731-1740.DOI: 10.3969/j.issn.1004-1524.20230833

• Crop Science • Previous Articles Next Articles

Identification of RcGeBP transcription factor and cloning and expression analysis of RcGeBP2 gene in castor

ZHU Guishuang(), LI Yanxiao, ZHANG Anning, SUN Haonan, XU Xingyuan, LI Zhigang, XIANG Dianjun()

College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, Inner Mongolia, China

Received:2023-07-05 Online:2024-08-25 Published:2024-09-06
Contact: XIANG Dianjun

Abstract

Abstract:

The GeBP gene family encodes a typical transcription factor that affects plant development and enhances plant survival in adverse environments by regulating the growth and differentiation of epidermal hairs. In order to explore the distribution of GeBP gene in the castor genome and the function of the characteristic gene RcGeBP2, all the GeBP genes of castor were identified in this paper. The RcGeBP2 gene was cloned by RT-PCR and its molecular characteristics were analyzed, including bioinformatics, subcellular localization and expression pattern.The results showed that four RcGeBP genes were unevenly distributed on three chromosomes in the genome of castor. The proteins encoded by RcGeBP genes were hydrophilic proteins, and the advanced structure was mainly random coil. The phylogenetic tree construction of GeBP showed that the GeBP protein of castor had the closest relationship with the GeBP protein of tomato. The GeBP gene of castor had three and two genome duplications with the GeBP gene of tomato and Arabidopsis thaliana, respectively. The results of Ka/Ks showed that the evolution of GeBP gene among species was passivated. The results of cis-acting element prediction showed that the RcGeBP promoter region contained multiple stress response and hormone-inducible elements.The FPKM expression value of RcGeBP genes showed that these genes had tissue expression characteristics and their expression was activated by drought and salt stress. The subcellular localization of RcGeBP2 protein showed that it was localized in the nucleus. In summary, this study has certain reference value for exploring the cross-regulation of castor RcGeBP gene family involved in salt and drought stress.

Key words: castor, GeBP, gene cloning, expression, subcellular localization

CLC Number:

ZHU Guishuang, LI Yanxiao, ZHANG Anning, SUN Haonan, XU Xingyuan, LI Zhigang, XIANG Dianjun. Identification of RcGeBP transcription factor and cloning and expression analysis of RcGeBP2 gene in castor[J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1731-1740.

Figures/Tables 13

References 24

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引物名称 Primer name	引物序列 Primer sequences(5'→3')	用途 Usage
RcGeBP2-F1	ATGGACTCCAATCTCAACCCACTCC	基因克隆Gene cloning
RcGeBP2-R1	TCATAACCTAACAGAACCCTCAAGC
RcGeBP2-F2	CTTCACTGTTGATACATATGGACTCCAATCTCAACCC	亚细胞定位Subcellular localization
RcGeBP2-R2	ATCCGGTACCCCCGGGTAACCTAACAGAACCCTCAAG

引物名称 Primer name	引物序列 Primer sequences(5'→3')	用途 Usage
RcGeBP2-F1	ATGGACTCCAATCTCAACCCACTCC	基因克隆Gene cloning
RcGeBP2-R1	TCATAACCTAACAGAACCCTCAAGC
RcGeBP2-F2	CTTCACTGTTGATACATATGGACTCCAATCTCAACCC	亚细胞定位Subcellular localization
RcGeBP2-R2	ATCCGGTACCCCCGGGTAACCTAACAGAACCCTCAAG

基因登录号 GenBank No.	基因 Gene	氨基酸数目 Number of amino acid	分子量 Molecular weight/u	等电点 pI	总平均疏水性 Grand average of hydropathicity	不稳定系数 Instability index	脂肪系数 Aliphatic index	带正电氨基酸 Positively charged amino acids (Arg+Lys)	带负电氨基酸 Negatively charged amino acids (Asp+Glu)	亚细胞位置 Subcellular localization
Rc05T009423	RcGeBP1	391	43637.68	5.32	-1.155	46.84	57.16	71	82	细胞核 Nucleus
Rc05T012306	RcGeBP2	286	32508.92	9.54	-0.706	58.59	77.31	42	33	细胞核 Nucleus
Rc09T020714	RcGeBP3	383	42740.10	5.00	-1.140	52.29	64.13	60	79	细胞核 Nucleus
Rc10T024212	RcGeBP4	415	46173.80	4.62	-0.770	62.28	74.75	46	76	细胞核 Nucleus

基因登录号 GenBank No.	基因 Gene	氨基酸数目 Number of amino acid	分子量 Molecular weight/u	等电点 pI	总平均疏水性 Grand average of hydropathicity	不稳定系数 Instability index	脂肪系数 Aliphatic index	带正电氨基酸 Positively charged amino acids (Arg+Lys)	带负电氨基酸 Negatively charged amino acids (Asp+Glu)	亚细胞位置 Subcellular localization
Rc05T009423	RcGeBP1	391	43637.68	5.32	-1.155	46.84	57.16	71	82	细胞核 Nucleus
Rc05T012306	RcGeBP2	286	32508.92	9.54	-0.706	58.59	77.31	42	33	细胞核 Nucleus
Rc09T020714	RcGeBP3	383	42740.10	5.00	-1.140	52.29	64.13	60	79	细胞核 Nucleus
Rc10T024212	RcGeBP4	415	46173.80	4.62	-0.770	62.28	74.75	46	76	细胞核 Nucleus

蛋白质名称 Protein name	α螺旋 α-Helix	β折叠 β-Sheet	无规卷曲 Random coil	延伸链 Extended strand
RcGeBP1	40.41	3.07	53.96	2.56
RcGeBP2	39.16	4.20	48.25	8.39
RcGeBP3	40.99	2.35	51.17	5.48
RcGeBP4	37.59	2.65	46.99	12.77

Identification of RcGeBP transcription factor and cloning and expression analysis of RcGeBP2 gene in castor

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Figures/Tables 13

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共线基因名称 Collinear gene name	非同义替换率 Ka	同义替换率 Ks	非同义替换率/ 同义替换率 Ka/Ks
RcGeBP1_Solyc05g051330.1	0.651	-	-
RcGeBP2_Solyc07g052830.2	0.390	2.308	0.169
RcGeBP3_Solyc07g052900.1	0.530	2.510	0.211
RcGeBP1_AEE85025.1	0.449	-	-
RcGeBP1_AEE82001.1	0.336	1.702	0.198

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