亚麻生氰糖苷合成关键酶CYP79基因家族的鉴定及表达分析

doi:10.3724/SP.J.1006.2023.24042

Abstract

Abstract:

CYP79 is a key enzyme in the synthesis of cyanogenic glycoside. However, there is no systematical study of CYP79 genes in flax. In this study, we identified CYP79 gene family in 9 crops including flax, and focused on the sequence characteristics, duplication events, collinearity, evolution, cis-acting elements and expression patterns of LuCYP79 genes. The results revealed that a total of 9, 9, 3, 2, 5, 7, 6, 16, and 4 CYP79 family members were identified in flax, pale flax, poplar, cassava, sesame, sorghum, soybean, grape, and rice, respectively. Phylogenetic analysis showed that the evolution of CYP79 genes was species-specific. LuCYP79 were distributed unevenly on four chromosomes and had 1-3 exons. The promoter region of LuCYP79 contained lots of elements involved in response to hormone and stress. 8 full-length DNA sequences and 5 full-length cDNA sequences of flax LuCYP79 genes were cloned. LuCYP79 proteins contained 282-565 amino acid residues with molecular weight of 31.56-62.86 kD, and isoelectric point of 5.84-9.14. All LuCYP79 members were hydrophilic protein and located in endoplasmic reticulum. There were five pairs of LuCYP79 genes with duplication events, accounting for 77.8% of all genes, and all the duplication genes underwent strong purification selection. Both LuCYP79-1 and LuCYP79-9 had homologous genes in Arabidopsis and cassava. The relative expression levels showed that LuCYP79 family members were tissue-specific and had different expression patterns under different genetic backgrounds. There were significantly different in the relative expression of LuCYP79-1, LuCYP79-7, LuCYP79-8, and LuCYP79-9 in the four cultivars. Moreover, correlation analysis showed that LuCYP79-1/LuCYP79-7 in 50 days flaxseed was significantly positively correlated with the concentration of cyanogenic glycosides in mature flaxseed. LuCYP79-7/LuCYP79-8 and (LuCYP79-7+LuCYP79-9)/LuCYP79-8 in 20 days flaxseed were significantly positively correlated with the concentration of cyanogenic glycosides in mature flaxseed, respectively. It was preliminarily speculated that they might be the key genes in the synthesis of cyanogenic glycoside in flaxseed. These results have positive significance for further elucidating the function of CYP79 proteins in flax and provide theoretical references for breeding flax varieties with low cyanogenic glycoside.

Key words: flax, CYP79 gene family, cyanogenic glycoside, bioinformatics, the relative expression level

QI Yan-Ni, LI Wen-Juan, ZHAO Li-Rong, LI Wen, WANG Li-Min, XIE Ya-Ping, ZHAO Wei, DANG Zhao, ZHANG Jian-Ping. Identification and expression analysis of CYP79 gene family, a key enzyme for cyanogenic glycoside synthesis in flax[J].Acta Agronomica Sinica, 2023, 49(3): 687-702.

Figures/Tables 21

Table S1

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Table 1

Table S3

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Table 2

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Table 3

Predicted cis-acting elements of LuCYP79 promoters"

顺式元件Cis-element	典型序列 Typical sequence	特性 Characteristic	基因 Gene name
ARE	AAACCA	厌氧诱导必需的顺式作用元件 Cis-acting regulatory element essential for the anaerobic induction	LuCYP79-1, LuCYP79-2, LuCYP79-3, LuCYP79-4, LuCYP79-5, LuCYP79-6, LuCYP79-7, LuCYP79-8, LuCYP79-9
G-box	CACGTG/TACGTG	光响应顺式作用元件 Cis-acting regulatory element involved in light responsiveness	LuCYP79-1, LuCYP79-2, LuCYP79-3, LuCYP79-4, LuCYP79-5, LuCYP79-6, LuCYP79-7, LuCYP79-8, LuCYP79-9
GT1-motif	GGTTAAT/GGTTAA	光响应元件 Light responsive element	LuCYP79-1, LuCYP79-2, LuCYP79-3, LuCYP79-4, LuCYP79-5, LuCYP79-6, LuCYP79-7, LuCYP79-9
Box 4	ATTAAT	光响应保守模块的一部分 Part of a conserved DNA module involved in light responsiveness	LuCYP79-1, LuCYP79-2, LuCYP79-3, LuCYP79-5, LuCYP79-6, LuCYP79-7, LuCYP79-8, LuCYP79-9
GATA-motif	GATAGGG	光响应元件的一部分 Part of a light responsive element	LuCYP79-1, LuCYP79-3, LuCYP79-5, LuCYP79-7, LuCYP79-8, LuCYP79-9
ABRE	CGTACGTGCA/ CGCACGTGTC	脱落酸响应顺式元件 Cis-acting element involved in the abscisic acid responsiveness	LuCYP79-1, LuCYP79-2, LuCYP79-3, LuCYP79-4, LuCYP79-5, LuCYP79-6, LuCYP79-7, LuCYP79-8, LuCYP79-9
TGACG-motif	TGACG	MeJA响应顺式作用元件 Cis-acting regulatory element involved in the MeJA-responsiveness	LuCYP79-1, LuCYP79-2, LuCYP79-3, LuCYP79-4, LuCYP79-5, LuCYP79-6, LuCYP79-7, LuCYP79-8
CGTCA-motif	CGTCA	MeJA响应顺式作用元件 Cis-acting regulatory element involved in the MeJA-responsiveness	LuCYP79-1, LuCYP79-2, LuCYP79-3, LuCYP79-4, LuCYP79-5, LuCYP79-6, LuCYP79-7, LuCYP79-8
TGA-element	AACGAC	生长素响应元件 Auxin-responsive element	LuCYP79-1, LuCYP79-2, LuCYP79-5, LuCYP79-8
AuxRR-core	GGTCCAT	生长素响应顺式作用元件 Cis-acting regulatory element involved in auxin responsiveness	LuCYP79-4, LuCYP79-5
AuxRE	TGTCTCAATAAG	生长素响应元件的一部分 Part of an auxin-responsive element	LuCYP79-7
GARE-motif	TCTGTTG	赤霉素响应元件 Gibberellin-responsive element	LuCYP79-2, LuCYP79-9
P-box	CCTTTTG	赤霉素响应元件 Gibberellin-responsive element	LuCYP79-2
顺式元件Cis-element	典型序列 Typical sequence	特性 Characteristic	基因 Gene name
LTR	CCGAAA	低温响应顺式作用元件 Cis-acting element involved in low-temperature responsiveness	LuCYP79-1, LuCYP79-2, LuCYP79-4, LuCYP79-6, LuCYP79-7
MBS	CAACTG	参与干旱诱导的MYB结合位点 MYB binding site involved in drought-inducibility	LuCYP79-1, LuCYP79-2, LuCYP79-8, LuCYP79-9
TC-rich repeats	GTTTTCTTAC	参与防御和胁迫响应的顺式作用元件 Cis-acting element involved in defense and stress responsiveness	LuCYP79-2
RY-element	CATGCATG	参与种子特异性调控的顺式调控元件 Cis-acting regulatory element involved in seed-specific regulation	LuCYP79-4, LuCYP79-5, LuCYP79-7
CAT-box	GCCACT	分生组织相关的顺式调控元件 Cis-acting regulatory element related to meristem expression	LuCYP79-5, LuCYP79-6, LuCYP79-7
A-box	CCGTCC	顺式调控元件 Cis-acting regulatory element	LuCYP79-3, LuCYP79-7
GC-motif	CCCCCG	参与缺氧特异性诱导的类增强子元件 Enhancer-like element involved in anoxic specific inducibility	LuCYP79-1, LuCYP79-7
O2-site	GATGA(C/T)(A/G)TG (A/G)/GATGATGTGG	参与玉米醇溶蛋白新陈代谢调节的顺式调控元件 Cis-acting regulatory element involved in zein metabolism regulation	LuCYP79-1, LuCYP79-2, LuCYP79-6
MBSI	TTTTTACGGTTA	参与黄酮类合成基因调控的MYB结合位点 MYB binding site involved in flavonoid biosynthetic genes regulation	LuCYP79-3
HD-Zip 1	CAAT(A/T)ATTG	参与栅栏叶肉细胞分化的元件 Element involved in differentiation of the palisade mesophyll cells	LuCYP79-1

Table 3

Fig. 6

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Fig. 11

References 41

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基因名称 Gene name	正向引物序列 Forward sequence (5'-3')	反向引物序列 Reverse sequence (5'-3')
LuCYP79-1	ATGAACATCGACGGCCAGGAGAAG	TCAGTTGGTAATCTTGGGGTACAAGTG
LuCYP79-2	ATGACCATGAAAACCTCCGACG	TCAGTTGGTAACCAAAGGGTACAAG
LuCYP79-3	ATGCCCATGAACACCTCCGACCGAT	TCAGTTGGTAATCTTGGGGTACAAGTGG
LuCYP79-4	ATGAAGTCATCTCCGATCAACACTATTAC	TCATTTGGTAGAGCGGCTGGGTAC
LuCYP79-5	ATGGCAAATAACCTCCCTCCGAG	TCATTTGGCTAAGGCAGGGTACAAG
LuCYP79-6	ATGGAAACCATGATCCTCCTCGTC	TCAAGAGAGTGTAGGGTATAAATGAGG
LuCYP79-7	ATGAACACCTTCACAATCATCCTCC	TCATTTGACGACAACGACAGGGTAC
LuCYP79-8	ATGGCGGCCATGAACACCTCC	TCATTTGGCTAAGGCAGGGTACAAG
LuCYP79-9	ATGGCCATGAACACCTCCGAC	TCAGTTGGTAATCTTAGGGTACAAGTGGG

基因名称 Gene name	正向引物序列 Forward sequence (5'-3')	反向引物序列 Reverse sequence (5'-3')
LuCYP79-1	ACCGCTGCTGTCACTACCACG	CTGCTCCTTCTGATGCGTTGG
LuCYP79-2	GGGAAGGTGATTAAGGAGGCTAATAAG	CCACTGCGTTTGACGGGTTG
LuCYP79-3	GCAAGCGAATAAGACGATGAGGG	GGTTGGTGATTTCATTGCGGGAG
LuCYP79-4	CTCCGACCGATGTCTATCCACCAC	CCAGTCATAATGCTACCTGCTCCT
LuCYP79-5	CGGCACAATGACATCTACCACCTC	CTGCAATAAGCCTACCTGCTCTTC
LuCYP79-6	TAAGGAGTCGAATAAGGCGTTGC	CACTGCGTTGGATGGATTGTCTA
LuCYP79-7	CACCGCCGTCATAATCCTCCTC	GCCGCTGGCTTCTTCCTCGTT
LuCYP79-8	CGGACCGATGGAGATTGACC	TCCCTCGCACATGCCTTGAC
LuCYP79-9	TCTCACCGACGTTCTTATTACCCTT	GGACTAGCCTATCTTTACCGACCAC

基因名称 Gene name	基因号 Gene ID	染色体位置 Chromosome location	外显子数量 No. of exons	蛋白序列长度 Protein length (aa)	分子量 Molecular weight (kD)	等电点 pI	亚细胞定位 Subcellular location
LuCYP79-1	L.us.o.m.scaffold38.16	Chr2:4491546-4492641(+)	2	282	31.56	5.84	ER
LuCYP79-2	L.us.o.m.scaffold38.15	Chr2:4495863-4497662(+)	2	554	62.17	9.14	ER
LuCYP79-3	L.us.o.m.scaffold38.14	Chr2:4499744-4501641(+)	2	558	62.57	9.01	ER
LuCYP79-4	L.us.o.m.scaffold137.29	Chr6:18190484-18192183(+)	2	537	60.32	8.97	ER
LuCYP79-5	L.us.o.m.scaffold137.31	Chr6:18195750-18196883(+)	1	377	41.69	8.11	ER
LuCYP79-6	L.us.o.m.scaffold96.139	Chr12:3278067-3280521(-)	3	521	58.68	6.97	ER
LuCYP79-7	L.us.o.m.scaffold13.272	Chr12:15779026-15781011(-)	2	525	59.10	8.12	ER
LuCYP79-8	L.us.o.m.scaffold13.263	Chr12:15823701-15825571(+)	2	549	60.89	7.26	ER
LuCYP79-9	L.us.o.m.scaffold28.185	Chr15:6106894-6109113(-)	2	565	62.86	9.03	ER

物种 Species	基因号 Gene ID	物种 Species	基因号 Gene ID	物种 Species	基因号 Gene ID
白亚麻 Linum bienne	L.bie.m.scaffold143.40	芝麻 Sesamum indicum	rna5687	葡萄 Vitis vinifera	VIT_206s0009g01780.1
	L.bie.m.scaffold143.49		rna5689		VIT_206s0009g02820.1
	L.bie.m.scaffold349.34		rna5691		VIT_206s0009g02843.1
	L.bie.m.scaffold349.35		rna5692		VIT_206s0009g02850.1
	L.bie.m.scaffold349.36		rna9755		VIT_206s0009g02895.1
	L.bie.m.scaffold593.11	高粱 Sorghum bicolor	Sobic.001G012300.1.p		VIT_206s0009g02930.1
	L.bie.m.scaffold593.12		Sobic.001G185900.2.p		VIT_206s0009g02980.1
	L.bie.m.scaffold593.6		Sobic.001G185900.2.p		VIT_206s0009g03120.1
	L.bie.m.scaffold852.13		Sobic.001G187500.1.p		VIT_206s0009g03130.1
毛果杨 Populus trichocarpa	Potri.004G055200.1.p		Sobic.001G187600.1.p		VIT_213s0067g02720.1
	Potri.013G157200.1.p		Sobic.007G090457.1.p		VIT_213s0067g02730.1
	Potri.013G157400.1.p		Sobic.010G172200.1.p		VIT_213s0067g02780.1
木薯 Manihot esculenta	Manes.12G133500.1.p	大豆 Glycine max	Glyma.11G197300.1.p		VIT_213s0067g02790.1
木薯 Manihot esculenta	Manes.13G094200.1.p		Glyma.11G197400.1.p		VIT_213s0067g02830.1
水稻 Oryza sativa	LOC_Os03g37290.1		Glyma.13G051600.1.p		VIT_213s0106g00280.1
	LOC_Os04g08824.1		Glyma.18G052200.1.p		VIT_218s0001g13760.1
	LOC_Os04g08828.1		Glyma.20G065000.1.p
	LOC_Os04g09430.1		Glyma.20G065100.1.p

蛋白名称Protein name	α-螺旋 Alpha helix	β-转角 Beta turn	延伸链 Extended strand	无规则卷曲 Random coil
LuCYP79-9	120 (42.55%)	7 (2.48%)	35 (12.41%)	120 (42.55%)
LuCYP79-5	255 (46.03%)	22 (3.97%)	58 (10.47%)	219 (39.53%)
LuCYP79-4	240 (43.01%)	32 (5.73%)	86 (15.41%)	200 (35.84%)
LuCYP79-7	231 (43.02%)	23 (4.28%)	71 (13.22%)	212 (39.48%)
LuCYP79-8	177 (46.95%)	9 (2.39%)	48 (12.73%)	143 (37.93%)
LuCYP79-6	240 (46.07%)	21 (4.03%)	64 (12.28%)	196 (37.62%)
LuCYP79-3	234 (44.57%)	19 (3.62%)	68 (12.95%)	204 (38.86%)
LuCYP79-2	243 (44.26%)	21 (3.83%)	76 (13.84%)	209 (38.07%)
LuCYP79-1	247 (43.72%)	25 ( 4.42%)	76 (13.45%)	217 (38.41%)

Identification and expression analysis of CYP79 gene family, a key enzyme for cyanogenic glycoside synthesis in flax

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基因对 Gene pairs	复制事件 Duplication event	非同义替换率 Ka	同义替换率 Ks	Ka/Ks	选择类型 Selection type	分歧时间 Divergence time (MYa)
LuCYP79-1/LuCYP79-2	串联复制 Tandem duplication	0.0722	0.6753	0.1069	纯化选择 Purifying selection	55.3525
LuCYP79-2/LuCYP79-3	串联复制 Tandem duplication	0.0678	0.6603	0.1027	纯化选择 Purifying selection	54.1230
LuCYP79-4/LuCYP79-5	串联复制 Tandem duplication	0.1213	1.1045	0.1098	纯化选择 Purifying selection	90.5328
LuCYP79-1/LuCYP79-9	片段复制 Segmental duplication	0.0055	0.0164	0.3354	纯化选择 Purifying selection	1.3443
LuCYP79-4/LuCYP79-8	片段复制 Segmental duplication	0.1277	1.0731	0.1190	纯化选择 Purifying selection	87.9590

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