藜麦NRT2基因家族的鉴定及表达分析

doi:10.7668/hbnxb.20193363

摘要/Abstract

摘要：

硝态氮是植物吸收氮素的2种主要形式之一,硝酸盐转运蛋白2(NRT2)在土壤中硝酸盐缺乏时发挥主导作用。为探究藜麦NRT2基因家族的特征和表达模式,利用生物信息学方法,对藜麦NRT2基因进行全基因组鉴定,并分析了其编码蛋白、染色体定位、基因结构、系统进化、顺式作用元件、组织表达特异性以及不同氮素水平处理后基因的表达模式。结果表明,藜麦中有15个NRT2基因,分布在7条染色体上,每个成员分别含有1~9个内含子及2~10个外显子,蛋白亚细胞定位预测其均定位在质膜上,为疏水性蛋白。同时,系统进化分析显示,藜麦NRT2蛋白家族属于2个亚家族,与拟南芥的亲缘关系更近。顺式作用元件分析显示,藜麦NRT2家族成员启动子区存在大量与生长发育及逆境胁迫等相关的顺式作用元件。藜麦NRT2基因家族成员在不同组织器官中的表达存在差异,在根、茎、叶中表达量较高。在低氮条件下,藜麦NRT2.4、NRT2.7、NRT2.15表达上调;0,25%N处理后藜麦NRT2.7、NRT2.15的表达量急剧增加。研究结果可为后续藜麦NRT2s基因克隆和功能以及氮素胁迫分析提供参考依据。

关键词: 藜麦, 硝酸盐, NRT2, 基因家族, 氮胁迫

Abstract:

Nitrate nitrogen is one of the two main form of nitrogen uptaken by plants.Nitrate transporter 2(NRT2)plays a leading role in nitrogen uptake under nitrate deficiency conditions.In order to explore characteristics and expression pattern of NRT2 gene in Chenopodium quinoa,in the present study,fifteen members of C.quinoa NRT2s were identified based on bioinformatics analysis,and their encoding protein,chromosome location,gene structure,systematic evolution,promoter elements,tissue expression specificity and expression profile under different nitrogen levels were analyzed.The results showed that 15 NRT2s of C.quinoa were distributed on 7 chromosomes,each member contained 1-9 introns and 2-10 exons,respectively.These C.quinoa NRT2 proteins were predicted to be located on plasma membrane and belong to hydrophobic proteins.The evolutionary analysis found that the NRT2 protein family of quinoa belonged to two subfamilies,and they showed closer relationship to Arabidopsis thaliana.The cis-acting element analysis exhibited that the promoter regions of NRT2 had elements related to growth and stress responses.NRT2s showed varied expression profile in different C.quinoa tissues where more CqNRT2 members were higher expressed in roots,stems and leaves than those in other organs.The expression of CqNRT2.4,CqNRT2.7 and CqNRT2.15 was up-regulated under low nitrogen conditions where the expression levels of CqNRT2.7 and CqNRT2.15 were up-regulated sharply with 0 and 25% nitrogen treatment.The study might provide a reference basis for subsequent cloning,functional and nitrogen stress analysis of CqNRT2s gene.

Key words: Chenopodium quinoa, Nitrate, Nitrate transporter 2, Gene family, Nitrogen stress

杨利艳, 高源, 朱满喜, 邓妍, 王创云. 藜麦NRT2基因家族的鉴定及表达分析[J]. 华北农学报, 2022, 37(S1): 8-18. doi: 10.7668/hbnxb.20193363.

YANG Liyan, GAO Yuan, ZHU Manxi, DENG Yan, WANG Chuangyun. Identification and Expression Analysis of NRT2 Gene Family of Chenopodium quinoa[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(S1): 8-18. doi: 10.7668/hbnxb.20193363.

http://www.hbnxb.net/CN/Y2022/V37/IS1/8

图/表 11

表1 qRT-PCR引物序列

Tab.1 Primer sequences for qRT-PCR

基因 Gene	引物(5'-3') Primer(5'-3')	引物(5'-3') Primer(5'-3')	产物长度/bp Product size
18SrRNA	CAACCATAAACGATGCCGA	AGCCTTGCGACCATACTCC	112
CqNRT2.2	GGGTGTTACAGAAGAAGAC	CTCTCATTCCTACTGCCT	108
CqNRT2.4	AATTCGCCGAAGGTTGTAGG	AACATCAATCGCAGGACGG	89
CqNRT2.7	AGTACGATGACGACGAGAA	TTGTGTAGGTGGAGTAGCA	116
CqNRT2.15	GTCTTACCTACATGGGAGTCAT	AGCCTCCTCATTAGCATTCTTA	116

表2 藜麦NRT2家族基本信息

Tab.2 Basic information of NRT2 gene family in quinoa

基因ID Gene ID	基因名称 Gene name	编码序列长度/bp CDS length	等电点 pI	分子质量/ku MW	氨基酸数目/个 Amino acid number	不稳定系数 Instability index	总平均亲水性 Grand average of hydropathicity	跨膜结构域 Transmembrane domain
AUR62006663	CqNRT2.1	2 082	9.12	75.93	693	39.96	0.28	15
AUR62006662	CqNRT2.2	1 401	8.51	50.99	466	38.30	0.45	11
AUR62014088	CqNRT2.3	2 829	8.66	101.59	942	37.46	0.45	21
AUR62006661	CqNRT2.4	1 452	8.77	52.60	483	37.34	0.51	12
AUR62001493	CqNRT2.5	1 500	8.51	53.57	499	45.32	0.48	9
AUR62001495	CqNRT2.6	1 578	9.07	56.76	525	40.13	0.36	11
AUR62001496	CqNRT2.7	1 581	8.91	56.92	526	41.40	0.37	10
AUR62003509	CqNRT2.8	1 527	8.68	54.98	508	36.46	0.41	11
AUR62000316	CqNRT2.9	1 449	8.81	52.69	482	36.67	0.45	12
AUR62000317	CqNRT2.10	1 479	8.78	53.94	492	41.08	0.40	12
AUR62000318	CqNRT2.11	1 794	9.26	64.67	597	39.74	0.31	13
AUR62005427	CqNRT2.12	1 428	9.05	51.63	475	36.50	0.35	9
AUR62009877	CqNRT2.13	1 563	8.20	56.05	520	39.99	0.45	11
AUR62009875	CqNRT2.14	1 539	8.90	55.76	512	40.25	0.37	10
AUR62009874	CqNRT2.15	1 581	8.71	56.94	526	39.83	0.37	10

图1 藜麦NRT2基因家族的染色体分布利用Phytozome数据库中藜麦基因组基因结构注释信息文件和TBtools软件,分析藜麦NRT2s基因的染色体定位。

Fig.1 Distribution of NRT2 gene family in quinoa on chromosome The chromosome localization of NRT2s gene in quinoa based on gene structure annotation of quinoa genome in Phytozome database and TBtools software.

表3 藜麦NRT2的亚细胞定位预测

Tab.3 Subcellular localization prediction of NRT2 in quinoa

蛋白名称 Protein name	细胞质膜 Plasma membrane	内质网 Endoplasmic reticulum	液泡膜 Vacuolar membrane	叶绿体 Chloroplast	高尔基体 Golgi	细胞质 Cytoplasm	细胞核 Nucleus	线粒体 Mitochondrion
CqNRT2.1	9	2	-	2	-	-	-	1
CqNRT2.2	9	1	2	-	-	1	-	-
CqNRT2.3	11	1	-	-	2	-	-	-
CqNRT2.4	10	3	1	-	-	-	-	-
CqNRT2.5	11	-	1	-	1	1	-	-
CqNRT2.6	8	1	3	-	-	1	-	-
CqNRT2.7	8	-	4	-	-	1	-	-
CqNRT2.8	7	1	3	-	3	-	-	-
CqNRT2.9	9	4	1	-	-	-	-	-
CqNRT2.10	8	3	2	-	-	-	-	-
CqNRT2.11	9	3	-	1	-	-	-	1
CqNRT2.12	10	1	1	-	1	-	1	-
CqNRT2.13	9	-	2	-	2	2	-	-
CqNRT2.14	8	2	3	-	1	-	-	-
CqNRT2.15	7	1	4	-	-	1	-	-

图2 藜麦NRT2基因结构及motif分析 A.藜麦NRT2基因结构分析:黄色矩形.非编码区(UTR),绿色矩形.编码序列(CDS),比例尺代表基因序列长度;B.藜麦NRT2蛋白Motif分析:不同颜色的矩形代表不同的蛋白保守基序,比例尺代表蛋白序列长度。

Fig.2 Gene structure and motif analysis of NRT2 in quinoa A.Gene structure analysis of NRT2s in quinoa:Yellow rectangles.Untranslated region(UTR),Green rectangles.Coding sequence(CDS),the scale bar indicates the length of gene sequence;B.Motif analysis of NRT2 proteins in quinoa:Rectangles with different colors represent conserved motifs of different proteins,the scale bar shows the length of protein sequence.

图3 藜麦、拟南芥、水稻和玉米NRT2蛋白系统进化树 ▲.藜麦NRT2蛋白;●.拟南芥NRT2蛋白;◆.水稻NRT2蛋白;■.玉米NRT2蛋白。从TAIR和Phytozome数据库分别获得拟南芥(At)、水稻(Os)、玉米(Zm)和藜麦(Cq)NRT2蛋白序列。采用ClustalW软件进行序列比对,用邻接法构建系统发育树。

Fig.3 Phylogenetic tree of NRT2 proteins in Chenopodium quinoa, Arabidopsis thaliana, Oryza sativa and Zea mays ▲.NRT2 proteins of Chenopodium quinoa;●.NRT2 proteins of Arabidopsis thaliana;◆.NRT2 proteins of Oryza sativa;■.NRT2 proteins of Zea mays.NRT2 protein sequences of Arabidopsis thaliana (At),Zea mays (Zm)and Chenopodium quinoa (Cq)were obtained from TAIR and Phytozome database,respectively.The phylogenetic tree was constructed by neighbor joining method with ClustalW.

表4 藜麦NRT2启动子顺式作用元件分析

Tab.4 Analysis of cis-acting elements of NRT2 promoters in quinoa

基因名称 Gene name	植物激素调节元件 Plant hormone regulatory elements						生长发育调节元件 Growth and development regulatory elements					逆境胁迫响应元件 Adversity stress response element					光响应元件 Light-responsive elements
基因名称 Gene name	茉莉酸甲酯 MeJA	脱落酸 ABA	乙烯 ETH	水杨酸 SA	生长素 Auxin	赤霉素 GA	昼夜节律 Circadian rhythm	分生组织表达 Meristem expression	胚乳发育 Endosperm development	根发育 Root development	种子发育 Seed development	厌氧 Anaerobic	低温 LT	病菌 Pathogen	干旱 Drought	防御和应激 Defense and stress	光反应 Light- responsive
CqNRT2.1	3	2	-	-	-	1	-	-	-	-	-	-	-	2	1	-	5
CqNRT2.2	1	2	2	2	-	-	1	1	-	-	-	-	-	-	-	-	7
CqNRT2.3	3	-	-	-	1	-	-	-	-	-	-	1	2	-	-	-	4
CqNRT2.4	2	1	-	-	1	-	1	-	-	-	1	3	1	-	-	-	6
CqNRT2.5	1	2	-	-	-	-	-	1	-	-	-	-	1	-	-	-	5
CqNRT2.6	-	3	-	-	-	1	-	-	1	1	-	3	1	-	3	-	7
CqNRT2.7	1	4	-	-	-	-	-	-	-	-	-	3	-	-	-	1	15
CqNRT2.8	2	2	-	-	-	-	-	-	-	-	-	3	-	-	-	1	8
CqNRT2.9	-	-	-	-	-	-	-	-	-	-	-	3	2	-	-	-	3
CqNRT2.10	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	-	18
CqNRT2.11	3	-	-	-	-	1	-	-	1	-	-	3	-	2	-	-	10
CqNRT2.12	1	2	-	1	-	-	-	-	-	-	-	-	-	1	-	1	10
CqNRT2.13	-	-	-	-	-	-	-	1	-	-	-	-	-	-	1	-	3
CqNRT2.14	1	2	-	-	-	-	1		-	-	-	2	-	-	2	-	7
CqNRT2.15	-	-	-	-	-	-	-	1	-	-	-	1	-	1	-	-	8

图4 藜麦NRT2基因组织特异性表达热图不同颜色代表不同表达量。

Fig.4 Tissue specific expression heat map of quinoa NRT2s Different colors represent different expression of NRT2s.

图5 不同氮素水平处理下藜麦根、叶中NRT2s的表达热图不同颜色代表不同表达量。CK 5 d/30 d: 全营养处理5 d/30 d;LN 5 d/30 d: 低氮处理55 d/30 d;NS 5 d/30 d: 氮饥饿处理5 d/30 d。

Fig.5 Expression heat map of NRT2s in quinoa root and leaf under different nitrogen levels Different colors represent different expression of NRT2s.CK 5 d/30 d: Plants were treated with total nutrients for 5 or 30 days;LN 5 d/30 d: Plants were treated with low nitrogen nutrition for 5 or 30 days;NS 5 d/30 d: Plants were treated with nitrogen starvation for 5 or 30 days.

图6 不同氮素水平处理下藜麦根的生长状况 A.在0硝酸盐培养基上培养10 d后藜麦的根;B.在25%硝酸盐培养基上培养10 d后藜麦的根;C.在50%硝酸盐培养基上培养10 d后藜麦的根;D.在75%硝酸盐培养基上培养10 d后藜麦的根;E.在CK(对照组)硝酸盐培养基上培养10 d后藜麦的根。

Fig.6 Growth status of quinoa root treated with different nitrogen A.Quinoa roots grew on 0 nitrate medium for 10 days;B.Quinoa roots grew on 25% nitrate medium for 10 days;C.Quinoa roots grew on 50% nitrate medium for 10 days;D.Quinoa roots grew on 75% nitrate medium for 10 days;E.Quinoa roots grew on CK(control group)nitrate medium for 10 days.

图7 不同氮素水平处理下CqNRT2.2、CqNRT2.4、CqNRT2.7、CqNRT2.15基因的qRT-PCR表达分析字母 a、b、c表示不同样本之间存在显著差异(P<0.05)。

Fig.7 Expression analysis of CqNRT2.2,CqNRT2.4,CqNRT2.7 and CqNRT2.15 under different nitrogen levels with qRT-PCR a,b,and c showed significant difference between different samples (P<0.05).

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