Identification and Expression Pattern Analysis of GmHMGS Gene in Soybean

doi:10.13560/j.cnki.biotech.bull.1985.2023-1102

Abstract

Abstract:

【Objective】3-hydroxy-3-methylglutaryl-CoA synthase（HMGS）is a key enzyme in the mevalonate pathway and plays an important role in the growth, development and synthesis of terpenoids. Bioinformatics study and expression pattern analysis of the GmHMGS gene can lay the foundation for exploring the function of GmHMGS gene. 【Method】The gene was identified and analysed using bioinformatics approaches, and then its expression pattern was examined using real-time fluorescence quantitative PCR（RT-qPCR）. 【Result】The GmHMGS gene had six family members in total, named GmHMGS1 to GmHMG6. The analysis of physicochemical properties and gene structure showed that GmHMGS3, GmHMG4, GmHMGS5, GmHMGS6 were stable hydrophilic proteins, and all GmHMGS possessed conserved functional domains of HMG-CoA synthase. Promoter sequence analysis revealed that GmHMGS has hormone and adversity stress related action elements. The analysis of tissue expression pattern revealed that GmHMGS was expressed in roots, stems, leaves, flowers, grains, pod skins, and root nodules, with leaves having the highest relative expression of GmHMGS1, GmHMG2, GmHMG3, GmHMG5, and GmHMG6, and roots having the highest relative expression of GmHMGS4. The GmHMGS genes were responsive to PEG6000, NaCl, and H₂O₂ stresses, as well as MeJA and ABA exogenous hormones, and the relative expression of GmHMGS1 and GmHMGS6 was higher under a wide range of adversity stresses, according to expression analysis under abiotic stress and different exogenous hormone-induced conditions. 【Conclusion】GmHMGS gene family may be involved in response to drought, oxidative and salt stresses in soybean.

Key words: soybean, GmHMGS, biocredit analysis, expression analysis, stress treatment

LOU Yin, GAO Hao-jun, WANG Xi, NIU Jing-ping, WANG Min, DU Wei-jun, YUE Ai-qin. Identification and Expression Pattern Analysis of GmHMGS Gene in Soybean[J]. Biotechnology Bulletin, 2024, 40(4): 110-121.

Figures/Tables 11

Table 1 Primers sequences for real-time quantitative PCR

基因名称Gene name	登录号Gene ID	正向引物Forward primer（5'-3'）	反向引物Reverse primer（5'-3'）
GmActing	XM_003552652	GGTGGTTCTATCTTGGCATC	CTTTCGCTTCAATAACCCTA
GmHMGS1	Glyma.01G215500.1	GGAGGAACTGCTGCTCTGTT	GGGCAGGTCCTTCAGCATAG
GmHMGS2	Glyma.05G050300.1	TCCAGTGGTTGATGGGAAGC	CCTCATCCACAAAACTGGCAT
GmHMGS3	Glyma.09G148500.1	GAGTAGCTCATGGGATGGACG	TAGGAGCATCTGGCCCTACA
GmHMGS4	Glyma.11G027000.1	AACATGTACACGGCGTCTCT	ATGGTGGCAGTTAAGCCACT
GmHMGS5	Glyma.16G200200.1	ATGCTATGGAGGAACGGCTG	ATCTGGCCCTACAAGCATGG
GmHMGS6	Glyma.17G132300.1	CCAGCAAGTTGCAAAGCCTC	GATGCGGTGTACATGTTGCC

Table 2 Analysis of GmHMGS gene sequence information and physicochemical properties

基因名称 Gene name	基因ID Gene ID	基因全长 Gene length/bp	CDS序列 CDS sequence/bp	氨基酸数 Amino acid amounts	分子式 Molecular formula	分子量 Mw/kD	等电点 PI	不稳定系数 Instability index	亲水性平均值 GRAVY
GmHMGS1	Glyma.01G215500.1	5 336	1 416	471	C₂₃₄₀H₃₆₀₄N₆₀₆O₇₀₇S₂₃	72.80	6.20	40.17	-0.231
GmHMGS2	Glyma.05G050300.1	4 665	882	293	C₁₄₃₃H₂₂₂₃N₃₇₇O₄₃₃S₁₂	44.78	6.08	41.69	-0.178
GmHMGS3	Glyma.09G148500.1	6 211	1 374	457	C₂₂₆₆H₃₄₈₈N₅₈₄O₆₈₂S₂₅	70.45	5.90	39.37	-0.163
GmHMGS4	Glyma.11G027000.1	6 456	1 428	475	C₂₃₄₄H₃₆₂₅N₆₀₅O₇₁₈S₂₂	73.14	5.77	39.33	-0.224
GmHMGS5	Glyma.16G200200.1	6 465	1 365	454	C₂₂₃₈H₃₄₄₀N₅₇₈O₆₈₀S₂₅	69.61	5.78	36.97	-0.174
GmHMGS6	Glyma.17G132300.1	4 760	1 383	460	C₂₂₈₇H₃₅₃₄N₅₈₈O₆₉₄S₂₂	71.25	5.98	39.33	-0.246

Fig. 1 Analysis of GmHMGS gene structure

Table 3 Prediction of secondary structure and subcellular localization of GmHMGS

蛋白名称Protein name	α螺旋Alpha helix/%	延伸链Extended strand/%	无规则卷曲Random coil/%	染色体Chr.	亚细胞定位Subcellular localization
GmHMGS1	25.05	22.29	52.65	01	细胞核Nucleus
GmHMGS2	25.26	22.53	52.22	05	细胞核Nucleus
GmHMGS3	22.32	19.91	57.77	09	叶绿体Chloroplast
GmHMGS4	23.37	21.89	54.74	11	细胞核Nucleus
GmHMGS5	21.81	21.59	56.61	16	叶绿体Chloroplast
GmHMGS6	31.09	20.87	48.04	17	细胞核Nucleus

Fig. 2 Tertiary structure of GmHMGS protein

Fig. 3 Motif composition of the CmHMGS gene A: GmHMGS conserved element analysis, Motif 1-6 in different colored blocks indicate the motif composition, B: Sequence of conserved structural elements of GmHMGS proteins

Fig. 4 Analysis of promoter cis-acting elements of the GmHMGS gene ABRE: Abscisic acid response element; ARFs: growth factor response elements; GARE-motif: gibberellin response element; G-box: light-responsive element; TCA-element: salicylic acid response element; MBS: Drought stress response element; ARE: anaerobic recovery element; LTR: low temperature response element; HSE: stress response element

Fig. 5 Analysis of the phylogenetic evolution of GmHMGS proteins

Fig. 6 Expression analysis of the GmHMGS gene family in different tissues Different letters indicate significant differences at the P <0.05 level

Fig. 7 Expression patterns of GmHMGS gene in response to abiotic stress in soybean A: PEG6000 treatment; B: NaCl stress; C: H2O2 stress. The gene expression level of GmHMGS of the control at 0 h post-treatment was set to 1, and those of GmHMGS of the treatments were accordingly accounted and presented as the relative fold changes. The data indicate the mean ± SE of three replicates. Different letters indicate significant differences at the P <0.05 level

Fig. 8 Expression patterns of GmHMGS gene in response to hormone treatment in soybean A: MeJA treatment; B: ABA treatment. the gene expression level of GmHMGS of the control at 0 h post-treatment was set to 1, and those of GmHMGS of the treatments were accordingly accounted and presented as the relative fold changes. The data indicate the mean x±SE of three replicates. Different letters indicate significant differences at the P <0.05 level

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