Identification of SOD Family Genes in Chenopodium quinoa and Their Response to Mixed Saline-alkali Stress

doi:10.13304/j.nykjdb.2022.0558

Abstract

Abstract:

Superoxide dismutase （SOD） is a key enzyme in the antioxidant system of plants and plays a critical role in protecting plants from various biological and abiotic stresses. In this paper， using bioinformatics methods， 12 SOD genes were identified in quinoa by sequence alignment based on Arabidopsis SOD， which localized in the nucleus， microsomes and mitochondria， and distributed heterogeneously on 11 different chromosomes， and the tertiary structure of their encoded proteins showed that Cu/Zn-SODs were homodimers with Fe-SODs and Mn-SODs were homotetramers.The intron/exon distribution patterns of the CqSOD genes were different， with the number of introns ranging from 4 to 7， and the conserved motifs differing significantly. The phylogenetic relationships showed that the SOD proteins could be divided into 3 subfamilies： Cu/Zn-SODs， Fe-SODs and Mn-SODs. In addition， all CqFe-SODs and CqMn-SODs promoter regions contained abscisic acid（ABA）-responsive cis-elements， and CqSOD12 interacted with 11 CqSOD proteins and 4 CqCAT proteins. Expression profiling showed that the 12 CqSOD genes were strongly responsive to both mixed saline-alkali and nitroprusside. Above results laid the foundation for research on the role and molecular mechanism of SOD genes in plant development and stress response.

Key words: Chenopodium quinoa, SOD family genes, salt-alkaline stress, bioinformatics analysis, expression analysis

摘要：

超氧化物歧化酶（superoxide dismutase，SOD）是植物抗氧化系统的关键酶，在保护植物免受生物和非生物胁迫方面发挥重要作用。以拟南芥SOD为基础，通过序列比对在藜麦基因组中鉴定出12个SOD基因，分别定位于细胞核、微体及线粒体，在11条染色体上不均匀分布，其编码蛋白质三级结构显示Cu/Zn-SODs与Fe-SODs为同源二聚体，Mn-SODs为同源四聚体。CqSOD基因内含子/外显子分布模式不尽相同，内含子数介于4～7个，保守基序差异明显。系统发育关系显示，SOD蛋白可分为Cu/Zn-SODs、Fe-SODs及Mn-SODs 3个亚族。此外，所有的CqFe-SODs及CqMn-SODs启动子区都含有脱落酸激素反应顺式元件，CqSOD12与11个CqSOD蛋白及4个CqCAT蛋白存在相互作用。表达谱分析表明，12个CqSOD基因对混合盐碱及硝普钠均有较强响应。研究结果为SOD基因在植物发育和胁迫响应中的作用及分子机制研究奠定基础。

关键词: 藜麦, SOD家族基因, 盐碱胁迫, 生物信息学分析, 表达分析

CLC Number:

S519

Yurong DENG, Lian HAN, Jinlong WANG, Xinghan WEI, Xudong WANG, Ying ZHAO, Xiaohong WEI, Chaozhou LI. Identification of SOD Family Genes in Chenopodium quinoa and Their Response to Mixed Saline-alkali Stress[J]. Journal of Agricultural Science and Technology, 2024, 26(1): 28-39.

邓玉荣, 韩联, 王金龙, 韦兴翰, 王旭东, 赵颖, 魏小红, 李朝周. 藜麦SOD家族基因的鉴定及其对混合盐碱胁迫的响应[J]. 中国农业科技导报, 2024, 26(1): 28-39.

Figures/Tables 10

References 34

1	MILLER A. Superoxide dismutases: ancient enzymes and new insights [J]. FEBS Lett., 2012, 586(5): 585-595.
2	MITTLER R. ROS are good [J]. Trends Plant Sci., 2017, 22(1):11-19.
3	BAFANA A, DUTT S, KUMAR S, et al.. Superoxide dismutase: an industrial perspective [J]. Crit. Rev. Biotechnol., 2011, 31(1):65-76.
4	ZELKO I N, MARIANI T J, FOLZ R J. Superoxide dismutase multigene family: a comparison of the CuZn-SOD (SOD1), Mn-SOD (SOD2), and EC-SOD (SOD3) gene structures, evolution, and expression [J]. Free Radic. Biol. Med., 2002, 33(3):337-349.
5	TEPPERMAN J M, DUNSMUIR P. Transformed plants with elevated levels of chloroplastic SOD are not more resistant to superoxide toxicity [J]. Plant Mol. Biol., 1990, 14(4): 501-511.
6	SU W, RAZA A, GAO A, et al.. Genome-wide analysis and expression profile of superoxide dismutase (SOD) gene family in rapeseed (Brassica napus L.) under different hormones and abiotic stress conditions [J/OL]. Antioxidants (Basel), 2021, 10(8): 1182 [2022-06-03]. .
7	ABREU I A, CABELLI D E. Superoxide dismutases-a review of the metal-associated mechanistic variations [J]. Biochim. Biophys. Acta, 2010, 1804(2): 263-274.
8	SONG J, ZENG L, CHEN R, et al.. In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula [J/OL]. 3 Biotech., 2018, 8(8): 348 [2022-06-03]. .
9	魏婧, 徐畅, 李可欣, 等. 超氧化物歧化酶的研究进展与植物抗逆性[J].植物生理学报, 2020, 56(12): 2571-2584.
	WEI J, XU C, LI K X, et al.. Progress on superoxide dismutase and plant stress resistance [J]. Plant Physiol. J., 2020, 56(12):2571-2584.
10	ASENSIO A C, GIL-MONREAL M, PIRES L, et al.. Two Fe-superoxide dismutase families respond differently to stress and senescence in legumes [J]. J. Plant Physiol., 2012, 169(13):1253-1260.
11	HAN L M, HUA W P, CAO X Y, et al.. Genome-wide identification and expression analysis of the superoxide dismutase (SOD) gene family in Salvia miltiorrhiza [J/OL]. Gene, 2020, 742:144603[2022-06-03]. .
12	ZHANG X, ZHANG L T, CHEN Y Y, et al.. Genome-wide identification of the SOD gene family and expression analysis under drought and salt stress in barley [J]. Plant Growth Regul., 2021, 94(1): 49-60.
13	FENG K, YU J H, CHENG Y, et al.. The SOD gene family in tomato: identification, phylogenetic relationships, and expression patterns [J/OL]. Front. Plant Sci., 2016(7): 1279 [2022-06-03]. .
14	ZHOU Y, HU L F, WU H, et al.. Genome-wide identification and transcriptional expression analysis of cucumber superoxide dismutase (SOD) family in response to various abiotic stresses [J/OL]. Int. J. Genomics, 2017, 2017: 7243973 [2022-06-03]. .
15	MOLINA-RUEDA J J, TSAI C J, KIRBY E G. The Populus superoxide dismutase gene family and its responses to drought stress in transgenic poplar overexpressing a pine cytosolic glutamine synthetase (GS1a) [J/OL]. PLoS One, 2013, 8(2): e56421 [2022-06-03]. .
16	ZURITA-SILVA A, FUENTES F, ZAMORA P, et al.. Breeding quinoa (Chenopodium quinoa Willd.): potential and perspectives [J]. Mol. Breed., 2014, 34(1): 13-30.
17	赵颖, 魏小红, 李桃桃. 外源NO对混合盐碱胁迫下藜麦种子萌发和幼苗生长的影响[J]. 草业学报, 2020, 29(4): 92-101.
	ZHAO Y, WEI X H, LI T T. Efferts of exogenous nitric oxide on seed Emination and seedling growth of Chenopodium quinoa under complex saline-alkali stress [J]. Acta Pratac. Sin., 2020, 29(4): 92-101.
18	刘文瑜, 杨发荣, 黄杰, 等. NaCl 胁迫对藜麦幼苗生长和抗氧化酶活性的影响[J].西北植物学报, 2017, 37(9): 1797-1804.
	LIU W Y, YANG F R, HUANG J, et al.. Response of seedling growth and the activities of antioxidant enzymes of Chenopodium quinoa to salt stress [J]. Acta Bot. Bor-Occid. Sin., 2017, 37(9):1797-1804.
19	RUIZ K B, BIONDI S, MARTÍNEZ E A, et al.. Quinoa-a model crop for understanding salt-tolerance mechanisms in halophytes [J]. Plant Biosyst., 2016, 150(2): 357-371.
20	李美丽, 宿俊吉, 杨永林, 等. 陆地棉COI家族基因鉴定及在干旱和盐胁迫下的表达分析[J].中国农业科技导报, 2022, 24(4):63-74.
	LI M L, SU J J, YANG Y L, et al.. Identification of COl family genes and their expression in Gossypium hirsutum L. under drought and salt stress [J]. J. Agric. Sci. Technol., 2022, 24(4): 63-74.
21	LIVAK K J, SCHMITTGEN T D. Analysis of relative gene expression data using Real-time quantitative PCR [J]. Methods, 2002, 25(4): 402-408.
22	WANG T, SONG H, ZHANG B H, et al.. Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.) [J/OL]. 3 Biotech., 2018, 8(12): 486 [2022-06-03]..
23	DEHURY B, SARMA K, SARMAH R, et al.. In silico analyses of superoxide dismutases (SODs) of rice (Oryza sativa L.) [J]. J. Plant Biochem. Biotechnol., 2013, 22(1): 150-156.
24	GOSAVI G U, JADHAV A S, KALE A A, et al.. Effect of heat stress on proline, chlorophyll content, heat shock proteins and antioxidant enzyme activity in sorghum (Sorghum bicolor) at seedlings stage [J]. Indian J. Biotechnol., 2014, 13(13): 356-363.
25	XMHA B, QXC B, QI Y B, et al.. Genome-wide analysis of superoxide dismutase genes in Larix kaempferi [J]. Gene, 2019, 686: 29-36.
26	TANG Y H, BAO X X, ZHI Y L, et al.. Overexpression of a MYB family gene, OsMYB6, increases drought and salinity stress tolerance in transgenic rice [J/OL]. Front. Plant Sci., 2019(10): 168 [2022-06-03]. .
27	LIN Y L, LAI Z X. Superoxide dismutase multigene family in longan somatic embryos: a comparison of CuZn-SOD, Fe-SOD, and Mn-SOD gene structure, splicing, phylogeny, and expression [J]. Mol. Breeding, 2013, 32(3): 595-615.
28	WANG W, ZHANG X, DENG F, et al.. Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum [J/OL]. BMC Genomics, 2017,18(1):376 [2022-06-03]. .
29	FINK R C, SCANDALIOS J G. Molecular evolution and structure-function relationships of the superoxide dismutase gene families in angiosperms and their relationship to other eukaryotic and prokaryotic superoxide dismutases [J]. Arch. Biochem. Biophys., 2002, 399(1): 19-36.
30	XU G X, GUO C C, SHAN H Y, et al.. Divergence of duplicate genes in exon-intron structure [J]. Proc. Natl. Acad. Sci. USA, 2012, 109(4): 1187-1192.
31	GILL S S, TUTEJA N. Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants [J]. Plant Physiol. Biochem., 2010, 48(12): 909-930.
32	FENG X, LAI Z X, LIN Y L, et al.. Genome-wide identification and characterization of the superoxide dismutase gene family in Musa acuminata cv.Tianbaojiao (AAA group)[J/OL]. BCM Genomics, 2015, 16:823 [2022-06-03]. .
33	HU X X, HAO C Y, CHENG Z M, et al.. Genome-wide identification, characterization, and expression analysis of the grapevine superoxide dismutase (SOD) family [J/OL]. Int. J.Genomics, 2019:7350414 [2022-06-03]. .
34	PILON M, RAVET K, TAPKEN W. The biogenesis and physiological function of chloroplast superoxide dismutases [J]. Biochim. Biophys. Acta, 2011, 1807(8): 989-998.

处理 Treatment	盐分组成Salt composition
处理 Treatment	氯化钠NaCl/ （200 mmol·L^-1）	硫酸钠Na₂SO₄/ （200 mmol·L^-1）	碳酸氢钠NaHCO₃/ （200 mmol·L^-1）	碳酸钠Na₂CO₃/（200 mmol·L^-1）	硝普纳SNP/ （150 μmol·L^-1）
CK	0	0	0	0	-
A	1	1	0	0	-
B	1	2	1	0	-
C	1	9	9	1	-
D	1	1	1	1	-
E	9	1	1	9	-
CK+	0	0	0	0	+
A+	1	1	0	0	+
B+	1	2	1	0	+
C+	1	9	9	1	+
D+	1	1	1	1	+
E+	9	1	1	9	+

处理 Treatment	盐分组成Salt composition
处理 Treatment	氯化钠NaCl/ （200 mmol·L^-1）	硫酸钠Na₂SO₄/ （200 mmol·L^-1）	碳酸氢钠NaHCO₃/ （200 mmol·L^-1）	碳酸钠Na₂CO₃/（200 mmol·L^-1）	硝普纳SNP/ （150 μmol·L^-1）
CK	0	0	0	0	-
A	1	1	0	0	-
B	1	2	1	0	-
C	1	9	9	1	-
D	1	1	1	1	-
E	9	1	1	9	-
CK+	0	0	0	0	+
A+	1	1	0	0	+
B+	1	2	1	0	+
C+	1	9	9	1	+
D+	1	1	1	1	+
E+	9	1	1	9	+

基因 Gene	正向引物 Forward primer（5’-3’）	反向引物 Reverse primer（5’-3’）	退火温度 Tm/℃	产物长度 Amplicon size/bp
CqActin	CCCTCACCACTTTCCGATCT	TCCTCACCCTCACCCATTTT	62.6	62
CqSOD01	ACTGGGAATGTCTCGGGTCT	GTAGCGGTACCATCATCCCC	61.6	141
CqSOD02	AGGAGATGGCCCAACAACTG	GGCGAACTTCGTCTTCAGGA	61.8	89
CqSOD03	TGCTGGTGGAAGATTGGCTT	TGTGGTGACTCGGTGAACTG	62.7	107
CqSOD04	CGGAAGATGAAGTCCGGCAT	CACAAGGGCTCTACCGACAA	61.9	138
CqSOD05	TTCAGAGAGACATGCGGGTG	CAGCATGCACCACAATAGCC	62.3	111
CqSOD06	TCATCTCCGGCGCCAATAAC	GCCATGAAGACCAGGAGTGA	62.0	87
CqSOD07	GGGGCCTAAACACTTTTCGC	TCCAGGTTGCATGGATTCCC	63.1	125
CqSOD08	GGGGCCTAAACACTTTTCGC	CGGCTCCAAGGCATCAAATG	63.5	86
CqSOD09	GGAGTCACATTGGGGAGAGC	TCCAGGTTGCATGGATTCCC	62.2	90
CqSOD10	CGTACGACTATGGCGCTCTT	ACATGACCTCCGCCATTGAA	61.4	118
CqSOD11	GCTGGGCTTGGCTTGTTTAC	TGCTCCCAAACGTCGATAGT	63.5	140
CqSOD12	CGTACGACTATGGCGCTCTT	GATTCACATGACCTCCGCCA	63.2	114

基因 Gene	正向引物 Forward primer（5’-3’）	反向引物 Reverse primer（5’-3’）	退火温度 Tm/℃	产物长度 Amplicon size/bp
CqActin	CCCTCACCACTTTCCGATCT	TCCTCACCCTCACCCATTTT	62.6	62
CqSOD01	ACTGGGAATGTCTCGGGTCT	GTAGCGGTACCATCATCCCC	61.6	141
CqSOD02	AGGAGATGGCCCAACAACTG	GGCGAACTTCGTCTTCAGGA	61.8	89
CqSOD03	TGCTGGTGGAAGATTGGCTT	TGTGGTGACTCGGTGAACTG	62.7	107
CqSOD04	CGGAAGATGAAGTCCGGCAT	CACAAGGGCTCTACCGACAA	61.9	138
CqSOD05	TTCAGAGAGACATGCGGGTG	CAGCATGCACCACAATAGCC	62.3	111
CqSOD06	TCATCTCCGGCGCCAATAAC	GCCATGAAGACCAGGAGTGA	62.0	87
CqSOD07	GGGGCCTAAACACTTTTCGC	TCCAGGTTGCATGGATTCCC	63.1	125
CqSOD08	GGGGCCTAAACACTTTTCGC	CGGCTCCAAGGCATCAAATG	63.5	86
CqSOD09	GGAGTCACATTGGGGAGAGC	TCCAGGTTGCATGGATTCCC	62.2	90
CqSOD10	CGTACGACTATGGCGCTCTT	ACATGACCTCCGCCATTGAA	61.4	118
CqSOD11	GCTGGGCTTGGCTTGTTTAC	TGCTCCCAAACGTCGATAGT	63.5	140
CqSOD12	CGTACGACTATGGCGCTCTT	GATTCACATGACCTCCGCCA	63.2	114

基因登录号 Gene accession No.	基因名称 Gene name	氨基酸数 Size/aa	分子量 Molecular weight /kD	等电点 pI	不稳定指数Instability index	脂肪酸指数Aliphatic index	疏水性Hydrophobicity	亚细胞定位Subcellular localization	磷酸化位点数量Phosphorylation site number
AUR62000929	CqSOD01	152	15.26	5.28	15.37	76.91	-0.19	细胞质Cytoplasm	14
AUR62005041	CqSOD02	152	15.27	5.28	15.37	76.91	-0.21	细胞质Cytoplasm	11
AUR62014976	CqSOD03	287	29.96	8.34	41.28	78.61	-0.19	细胞质Cytoplasm	77
AUR62029152	CqSOD04	246	25.26	6.02	28.11	85.28	-0.01	细胞质Cytoplasm	56
AUR62032030	CqSOD05	157	16.01	6.38	22.92	87.52	-0.18	细胞质Cytoplasm	16
AUR62032721	CqSOD06	130	13.41	6.33	16.19	89.23	-0.16	细胞质Cytoplasm	16
AUR62001685	CqSOD07	262	29.89	8.33	38.29	81.15	-0.35	微体Microbody	36
AUR62010480	CqSOD08	280	31.65	6.19	35.50	69.71	-0.46	微体Microbody	25
AUR62020097	CqSOD09	262	30.00	7.73	39.44	82.63	-0.33	微体Microbody	34
AUR62030413	CqSOD10	281	31.66	6.40	36.42	70.85	-0.47	微体Microbody	31
AUR62024917	CqSOD11	295	32.43	8.80	37.17	93.63	-0.12	线粒体Mitochondrial	46
AUR62030627	CqSOD12	233	25.89	6.79	39.36	87.98	-0.35	线粒体Mitochondrial	30