Expression Analysis of the GH3 Gene Family in Nelumbo nucifera underHormonal and Abiotic Stresses

doi:10.13560/j.cnki.biotech.bull.1985.2024-0704

Abstract

Abstract:

Objective To characterize NnGH3 gene family in lotus (Nelumbo nucifera) and analyze their roles in abiotic stress, and to provide key candidate genetic resources for the breeding of new lotus varieties with stress resistance. Method Bioinformatics methods were used to identify the family members of acyl amides synthetase (GH3) from the whole genome of N. nucifera, and to conduct the detailed study on the phytochemical properties, chromosomal localization, tertiary structure prediction, systematic evolution, gene structure, collinearity relationships, and expression patterns of GH3 enzymes. RT-qPCR technology was applied to investigate the expression patterns of NnGH3 family genes under various stress conditions including low temperature(4℃), anaerobic conditions(submergence), salt stress(300 mmol/L NaCl), and exogenous hormone treatments(0.1 mmol/L IAA, 1 mmol/L JA, and 5 mmol/L SA). Result The fourteen NnGH3 family members were identified from the lotus genome, distributed on 5 chromosomes, and named sequentially as NnGH3.1 to NnGH3.14 based on their chromosomal locations. Their molecular weights ranged from 365 to 630 amino acids, theoretical isoelectric points were all less than 7, and acidic proteins were localized in the nucleus and cytoplasm. Cluster analysis revealed two groups, Group I and Group Ⅱ, within the GH3 family, with most members containing 3-4 exons and GH3 superfamily domains. Collinearity analysis indicated that 2 pairs of genes among the 14 lotus GH3 genes, 14 pairs with (Arabidopsis thaliana) GH3 genes, and 6 pairs with (Oryza sativa) GH3 genes presented collinear relationships. Promoter cis-acting element analysis showed a lot of light-, stress-, and hormone-responsive elements within this family. Expression analysis demonstrated that NnGH3 genes negatively responded to low temperature stress, with most members positively responded to SA treatments and salt stress, and specifically responded to IAA and JA treatments as well as anaerobic stress. Notably,genes NnGH3.4 and NnGH3.13 from Group Ⅱ, and NnGH3.3 from Group I, had the most significant expression changes across all treatments. Conclusion Fourteen NnGH3 family members are identified and divided into two groups, Group Ⅰ and Group Ⅱ, which all contain GH3 superfamily domains and are acidic proteins. NnGH3 family genes are specifically expressed under different exogenous hormone and abiotic stress conditions.

Key words: Nelumbo nucifera, GH3 gene family, bioinformatics, phytohormone, abiotic stresses, expression pattern

KUANG Jian-hua, CHENG Zhi-peng, ZHAO Yong-jing, YANG Jie, CHEN Run-qiao, CHEN Long-qing, HU Hui-zhen. Expression Analysis of the GH3 Gene Family in Nelumbo nucifera underHormonal and Abiotic Stresses[J]. Biotechnology Bulletin, 2025, 41(2): 221-233.

Figures/Tables 10

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序号 No.	基因名称 Gene name	正向引物 Forward primer （5′-3′）	反向引物 Reverse primer （5′-3′）
1	NnGH3.1	TCACTCAGTTCTGGCACCAC	TGCAAGACCCCCTTTCGTTT
2	NnGH3.2	GGCAACCCATGACTACGTGA	CTGTACGCCCATTAAGCCCA
3	NnGH3.3	GATGGTTCGAAGAGGTCGCA	GAGGTGTACAGGGCTTCCAG
4	NnGH3.4	CTCACGCCTGTGATGAACCT	CTGGTCTTGAAGTGGTCGCT
5	NnGH3.5	GGTTCGAAGAGGTGGCAGAA	AATCCGCATGGGAAGCAAGA
6	NnGH3.6	AGCGCCCATGTCGAATACTT	GGGTAATCCGCAGAGGATGG
7	NnGH3.7	CTAACGGGGAGGCATCAAGG	GACAGGCACCAGCAGGTTAT
8	NnGH3.8	CCTGACTTCCGCCAATCCTT	CTAGTTCAGGGTTGGGCCTG
9	NnGH3.9	GTCTGGACCAAGGGAAAGGG	CTCGCTGTACCAGACCACAA
10	NnGH3.10	GTACAAAGGGGAGGAGGCAC	GACGCTTGAACGTTGTCACC
11	NnGH3.11	ACTACGGAAGCTGGAGGACT	GGGCGTAGTCGTCGTAAGAG
12	NnGH3.12	CCTCTTGCTTCCCATGCAGA	ACCCTTGATCTGTAAGCGGC
13	NnGH3.13	AGTTCTGGAACTTCTGCGGG	ACCTGGCGTCTTTGTCTCTG
14	NnGH3.14	AGCCCCCATATGATCGTTGC	GATCGGTTCTGACTCAGCGT
15	NnACT	CTCCGTGTTGCCCCTGAAG	CCAGCAAGGTCCAACCGAAG

序号 No.	基因名称 Gene name	正向引物 Forward primer （5′-3′）	反向引物 Reverse primer （5′-3′）
1	NnGH3.1	TCACTCAGTTCTGGCACCAC	TGCAAGACCCCCTTTCGTTT
2	NnGH3.2	GGCAACCCATGACTACGTGA	CTGTACGCCCATTAAGCCCA
3	NnGH3.3	GATGGTTCGAAGAGGTCGCA	GAGGTGTACAGGGCTTCCAG
4	NnGH3.4	CTCACGCCTGTGATGAACCT	CTGGTCTTGAAGTGGTCGCT
5	NnGH3.5	GGTTCGAAGAGGTGGCAGAA	AATCCGCATGGGAAGCAAGA
6	NnGH3.6	AGCGCCCATGTCGAATACTT	GGGTAATCCGCAGAGGATGG
7	NnGH3.7	CTAACGGGGAGGCATCAAGG	GACAGGCACCAGCAGGTTAT
8	NnGH3.8	CCTGACTTCCGCCAATCCTT	CTAGTTCAGGGTTGGGCCTG
9	NnGH3.9	GTCTGGACCAAGGGAAAGGG	CTCGCTGTACCAGACCACAA
10	NnGH3.10	GTACAAAGGGGAGGAGGCAC	GACGCTTGAACGTTGTCACC
11	NnGH3.11	ACTACGGAAGCTGGAGGACT	GGGCGTAGTCGTCGTAAGAG
12	NnGH3.12	CCTCTTGCTTCCCATGCAGA	ACCCTTGATCTGTAAGCGGC
13	NnGH3.13	AGTTCTGGAACTTCTGCGGG	ACCTGGCGTCTTTGTCTCTG
14	NnGH3.14	AGCCCCCATATGATCGTTGC	GATCGGTTCTGACTCAGCGT
15	NnACT	CTCCGTGTTGCCCCTGAAG	CCAGCAAGGTCCAACCGAAG

基因名称 Gene name	基因ID Gene identifier	氨基酸数目 Amino acid amount	α螺旋 Alpha helix （Hh）/%	无规则卷曲Random coil （Cc）/%	延伸链 Extended strand （Ee）/%
NnGH3.1	Nn1g01814.2	586	34.64	57.85	7.51
NnGH3.2	Nn1g03776.1	621	34.14	60.39	5.48
NnGH3.3	Nn1g03969.3	590	32.88	59.49	7.63
NnGH3.4	Nn1g04653.2	599	36.06	58.76	5.18
NnGH3.5	Nn1g06683.3	595	34.62	55.63	9.75
NnGH3.6	Nn1g06894.2	616	36.04	59.25	4.71
NnGH3.7	Nn3g16244.1	630	40.48	54.60	4.92
NnGH3.8	Nn3g19075.2	587	34.58	57.24	8.18
NnGH3.9	Nn4g22107.1	615	36.91	57.24	5.85
NnGH3.10	Nn4g25867.1	603	36.15	58.71	5.14
NnGH3.11	Nn4g26117.1	579	38.51	53.71	7.77
NnGH3.12	Nn5g29859.2	592	29.73	59.63	10.64
NnGH3.13	Nn5g30464.6	595	34.45	60.84	4.71
NnGH3.14	Nn7g36856.1	365	22.78	58.89	18.33

基因名称 Gene name	基因ID Gene identifier	氨基酸数目 Amino acid amount	α螺旋 Alpha helix （Hh）/%	无规则卷曲Random coil （Cc）/%	延伸链 Extended strand （Ee）/%
NnGH3.1	Nn1g01814.2	586	34.64	57.85	7.51
NnGH3.2	Nn1g03776.1	621	34.14	60.39	5.48
NnGH3.3	Nn1g03969.3	590	32.88	59.49	7.63
NnGH3.4	Nn1g04653.2	599	36.06	58.76	5.18
NnGH3.5	Nn1g06683.3	595	34.62	55.63	9.75
NnGH3.6	Nn1g06894.2	616	36.04	59.25	4.71
NnGH3.7	Nn3g16244.1	630	40.48	54.60	4.92
NnGH3.8	Nn3g19075.2	587	34.58	57.24	8.18
NnGH3.9	Nn4g22107.1	615	36.91	57.24	5.85
NnGH3.10	Nn4g25867.1	603	36.15	58.71	5.14
NnGH3.11	Nn4g26117.1	579	38.51	53.71	7.77
NnGH3.12	Nn5g29859.2	592	29.73	59.63	10.64
NnGH3.13	Nn5g30464.6	595	34.45	60.84	4.71
NnGH3.14	Nn7g36856.1	365	22.78	58.89	18.33

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