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Omics & Biotechnology

Identification of Interaction Region Between LcMYB1 and Promoters of Anthocyanin Biosynthetic Genes LcDFR and LcUFGT1 in Litchi chinensis

  • LAI Biao 1, 2 ,
  • WANG Qi 1 ,
  • LUO Gangjun 1 ,
  • DU Lina 1 ,
  • WANG Huicong , 1, 3, *
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  • 1. School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, China
  • 2. Correlative Innovation Centre for Green Development in Wulingshan Region, Chongqing 408100, China
  • 3. College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
*WANG Huicong,E-mail:

Received date: 2020-05-31

  Request revised date: 2020-09-06

  Online published: 2021-09-09

Copyright

Copyright reserved © 2021. Office of Acta Agronomica Sinica All articles published represent the opinions of the authors, and do not reflect the official policy of the Chinese Medical Association or the Editorial Board, unless this is clearly specified.

Abstract

The accumulation of anthocyanins is one of the most important factors in determining the pericarp coloration of litchi. LcDFR (dihydroflavonol 4-reductase) and LcUFGT1 (UDP-glucose: flavonoid 3-O-glucosyltransferase) are two crucial enzymes in the anthocyanin biosynthesis pathway of litchi pericarp, and the activities and gene expressions directly affect litchi fruit coloration. Previous study showed that the expressions of LcDFR and LcUFGT1 were regulated by the LcMYB1 transcription factor. However, how LcMYB1 regulates the expression of the target genes, whether LcMYB1 binds to their promoter, which cis-element in the promoter is the binding site of LcMYB1 remain to be uncovered. In this study, the promoters of LcDFR (1927 bp) and LcUFGT1 (1584 bp) were cloned and analyzed respectively. Six candidate MYB binding sites and some other cis-elements such as light responsive elements and hormone related elements were predicted. The promoters of the two genes were then fragmented and ligated to pGreen-0800-luc plasmid to drive the expression of luciferase (LUC). Dual luciferase assay indicated that LcMYB1 could activate 904 bp to 1425 bp region of LcDFR promoter and 610 bp upstream of LcUFGT1 gene, which contain 1 and 2 candidate MYB-CORE sites, respectively. The interaction was also confirmed by the yeast one hybrid assay. These results suggested that LcMYB1 regulated the biosynthesis of anthocyanins by directly targeting the promoters of key structural genes and the binding region was narrowed down.

Cite this article

LAI Biao , WANG Qi , LUO Gangjun , DU Lina , WANG Huicong . Identification of Interaction Region Between LcMYB1 and Promoters of Anthocyanin Biosynthetic Genes LcDFR and LcUFGT1 in Litchi chinensis[J]. Chinese Journal of Tropical Crops, 2021 , 42(8) : 2151 -2157 . DOI: 10.3969/j.issn.1000-2561.2021.08.005

荔枝(Litchi chinensis Sonn.)属于无患子科荔枝属果树,是我国南方的特色水果之一,广受消费者喜爱。果实颜色是果品的重要外观品质指标,研究发现,随着荔枝果实逐渐成熟,荔枝果皮中叶绿素慢慢褪去,而花色苷不断合成从而呈现出鲜红色[1]。花色苷生物合成途径是类黄酮代谢途径的一个分支,参与花色苷生物合成的结构基因包括:查尔酮合成酶(Chalcone synthase, CHS)、查尔酮异构酶(Chalcone isomerase, CHI)、黄烷酮3-羟化酶(Flavanone 3-hydroxylase, F3H)、黄烷酮3′-羟化酶(Flavonoid 3′-hydroxylase, F3′H)、二氢黄酮醇4-还原酶(Dihydroflavonol 4-reductase, DFR)、花青素合成酶(Anthocyanidin synthase, ANS)和类黄酮糖基转移酶(UDP-glucose: flavonoid 3-O-glucosyltransferase, UFGT[2,3,4]
本课题组前期研究发现,荔枝果皮花色苷含量与大部分花色苷生物代谢相关酶活性正相关,特别是类黄酮糖基转移酶UFGT[1]。近年来,参与荔枝果皮花色苷生物合成的关键结构基因已经被克隆,表达分析结果显示结构基因LcDFRLcUFGT1的表达与花色苷含量成显著正相关关系,异源和同源转化实验均证实LcUFGT1在荔枝花色苷生物合成过程中起关键的作用[5,6,7]
自20多年前Paz-Ares等从玉米中发现MYB转录因子ZmC1基因以来,大量调控花色苷合成的关键MYB转录因子从各种草本植物和果实中得以分离鉴定[8,9]。研究发现,荔枝花色苷生物合成关键转录因子LcMYB1的表达水平与荔枝不同颜色品种果皮、不同组织和不同发育阶段果皮中花色苷含量成正相关,转LcMYB1烟草的花瓣和叶片中合成大量花色苷,同时烟草内源关键基因NtDFRNtANSNtUFGT的表达也大幅度提高[10]。然而,LcMYB1如何调控结构基因的表达以及转录激活结构基因启动子的具体结合区域尚待研究。
本研究利用基因组信息克隆了荔枝果皮花色苷生物合成的2个关键基因LcDFRLcUFGT1的启动子序列,进一步通过生物信息学手段预测了启动子区域的MYB结合位点和其他重要的顺式作用元件,并通过启动子5′ 端删减结合双荧光素酶和酵母单杂交的方法缩小了LcMYB1激活2个启动子的范围,为进一步探索LcMYB1结合启动子的具体顺式作用元件奠定基础。

1 材料与方法

1.1 材料

1.1.1 植物材料 ‘妃子笑’荔枝采自华南农业大学园艺学院教学实习基地,本氏烟草(Nicotiana benthamiana)种植于人工气候箱(22 ℃)。
1.1.2 菌株与载体 大肠杆菌(Escherichia coli)感受态细胞DH5α,购自宝日医生物技术(北京)有限公司公司;根癌农杆菌(Agrobacterium tumefaciens)菌株GV3101和植物瞬时表达载体pEAQ-MYB1由本实验室保存,pGreen-0800-luc由Roger P. Hellens教授(The New Zealand Institute of Plant and Food Research)馈赠;植物DNA提取试剂盒、胶回收试剂盒和质粒小提试剂盒,购自宝日医生物技术有限公司。

1.2 方法

1.2.1 DNA提取 取幼嫩的‘妃子笑’叶片为材料,用DNA提取试剂盒提取荔枝叶片基因组DNA,具体方法参见说明书。
1.2.2 启动子的克隆及生物信息分析 根据荔枝基因组信息(http://litchidb.genomics.cn/page/species/index.jsp),设计了特异引物DFRp-F和DFRp-R扩增LcDFR启动子,UFGTp-F和UFGTp-R扩增LcUFGT1启动子,引物序列见表1。用高保真酶PrimeSTAR® Max DNA Polymerase (Takara)以DNA为模板扩增LcDFRLcUFGT1基因的启动子。扩增的DNA片段利用Infusion技术(Takara)分别与用Nru I和Xho I双酶切线性化的pGreen-0800-luc连接。测序后,将得到的序列信息在软件PlantPAN2.0(http://plantpan2.itps.ncku.edu.tw/)和PlantCARE(http://bioinformatics.psb.ugent.be/webtools/plantcare/html/)上分析启动子上可能的顺式作用元件。
表1 用于扩增LcDFRLcUFGT1启动子片段的引物

Tab. 1 Primers used for amplify promoter fragments of LcDFR and LcUFGT1

引物名称
Primer Name
序列(5′-3′)
Sequences (5′-3′)
酶切位点
Restriction Site
用途
Function
DFRp-F TATAGGGCGAATTGGGTACCCTACTCTGGTTTAATTGGGAGC Knp I 荧光素酶实验
DFRp-R TAGAACTAGTGGATCCACACAGTCTCAGATTGTGATCCCAT BamH I 荧光素酶实验
UFGTp-F TATAGGGCGAATTGGGTACCTATACGAGCAAGAAAAGACTGAAGC Knp I 荧光素酶实验
UFGTp-R TAGAACTAGTGGATCCTATATACATATGTATAGACATGTATATG BamH I 荧光素酶实验
DFR-F2 TATAGGGCGAATTGGGTACCTCTGATCTCAACTAGGTTGAC Knp I 荧光素酶实验
DFR-F3 TATAGGGCGAATTGGGTACCATGTTGACTTTAACCCAACC Knp I 荧光素酶实验
DFR-F4 TATAGGGCGAATTGGGTACCCTTACATATACACCAGTTCG Knp I 荧光素酶实验
UFGTp-F2 TATAGGGCGAATTGGGTACCTACCTTATATCTGCCGGAAAGG Knp I 荧光素酶实验
UFGTp-F3 TATAGGGCGAATTGGGTACCAGTAAGGGCTGGATTAAGTG Knp I 荧光素酶实验
DFRpro-Y-F AAAGCTTGAATTCGAGCTCTCTGATCTCAACTAGGTTGACATCTGG Kpn I 酵母单杂交
DFRpro-Y-R CATACAGAGCACATGCCTAATTGATGGATCCTCAAATGGGTCTCCA Xho I 酵母单杂交
UFGTpro-Y-F AAAGCTTGAATTCGAGCTAGTAAGGGCTGGATTAAGTGAATAGGGG Kpn I 酵母单杂交
UFGTpro-Y-R CATACAGAGCACATGCCATATACATATGTATAGACATGTATATG Xho I 酵母单杂交
1.2.3 不同删减启动子片段扩增及双荧光素酶载体构建 为了研究LcMYB1能否与结构基因启动子结合及其具体的结合区域,对LcDFRLcUFGT1启动子进行了逐步删减处理,如图1所示。利用表1中的引物序列DFRp-F+DFRp-R、DFRp-F2+DFRp-R、DFRp-F3+DFRp-R、DFRp-F4+ DFRp-R分别扩增LcDFR基因上游1927、1425、904、433 bp到起始密码ATG的启动子的序列,得到4个启动子片段,分别为DFRp、DFRp1、DFRp2、DFRp3。同理,利用UFGTp- F+UFGTp-R、UFGTp-F2+UFGTp-R和UFGTp-F3+ UFGTp-R分别扩增了LcUFGT基因上游1580、1093、610 bp到起始密码的启动子序列,得到了3个启动子片段UFGTp、UFGTp1、UFGTp2(图1)。将得到的这些片段利用In-fusion技术分别于pGreen-0800- luc连接。将经测序正确后的载体利用热激法转化根癌农杆菌菌株GV3101备用。
图1 双荧光素酶实验分析LcMYB1激活LcDFRLcUFGT1启动子区域

A:不同大小启动子片段载体示意图;B:LcMYB1激活不同LcDFR启动子片段的活力;C:LcMYB1激活不同LcUFGT1启动子片段的活力。

Fig. 1 Transcriptional activation activities of LcMYB1 to the promoter of LcDFR and LcUFGT1 determined by dual luciferase assay

A: The promoter fragments of LcDFR and LcUFGT1; B: The activities of different fragments of LcDFR promoter; C: The activities of different fragments of LcUFGT promoter.

1.2.4 双荧光素酶实验 转录因子激活结构基因启动子的能力通过测定萤火虫荧光素酶(firefly luciferase, LUC)检测,用CaMV:35S驱动的海肾荧光素酶(renilla luciferase, REN)作为对照。用生长4~6周健康的本氏烟草叶片用于瞬时表达转录因子和启动子驱动的萤火虫荧光素酶。挑选根癌农杆菌在10 mL YEP中培养过夜,离心收集菌体,用注射缓冲液MAA[10 mmol/L MES(2-[N-morpholino]ethanesulfonic acid)pH 5.6,10 mmol/L MgCl2,100 μmol/L Acetosyringone]悬浮菌液至OD600为1.0左右。用注射器注射含有双荧光报告载体和瞬时表达载体pEAQ-LcMYB1的根癌农杆菌于烟草叶背面,并标记好注射范围,同时注射含pEAQ-HT的根癌农杆菌作为对照,瞬时表达和酶活力测定方法参见文献[11]。
1.2.5 酵母单杂交实验 酵母单杂交实验采用Clonteh公司的试剂盒Matchmaker™ Gold Yeast One-Hybrid System(Clontech)进行。LcDFR基因上游904 bp至1425 bp区域的序列经LcDFRpro-F和LcDFRpro-R扩增后,用In-fusion技术将启动子片段连接到用Kpn I和Xho I酶切线性化的pAbAi载体上。同理,LcUFGT1基因上游610 bp至ATG区域的序列经LcUFGTpro-F和LcUFGTpro-R扩增后连接到pAbAi载体上,引物序列见表1。将LcMYB1全长经Nde I和BamH I酶切位点连接到pGADT7(AD)载体上。构建好的LcMYB1-AD重组质粒分别经PEG/LiAC介导转入LcDFRpro和LcUFGTpro的酵母感受态细胞,涂布于SD/-Leu/AbA平板。30 ℃培养3~5 d,观察酵母生长情况。

2 结果与分析

2.1 LcDFR启动子的克隆及顺式作用元件分析

基于荔枝基因组信息,利用特异引物经过PCR扩增测序得到长度为1927 bp 的LcDFR启动子序列信息。将扩增测序的启动子序列分别在PlantPAN 2.0和PlantCARE数据库中进行搜索发现了大量的MYB可能结合位点。如表2所示,LcDFR启动子上存在3个MYB-CORE位点(CNGTTR)。此外,还发现LcDFR基因上游688 bp处有1个防御与胁迫响应元件(TC-rich repeats),在上游463 bp处有1个温度响应元件(LTR),上游1110 bp处有1个赤霉素响应元件,还有大量的光响应元件(表2)。
表2 LcDFR启动子预测的顺式作用元件

Tab. 2 Predicted cis-elements in promoter of LcDFR

顺式作用
元件
Site Name
位置
Position

Strand
序列(5′-3′)
Sequence (5′-3′)
预测的功能
Function
TC-rich
repeats
688 - ATTTTCTTCA Cis-acting element involved in defense and stress responsiveness
LTR 463 + CCGAAA Cis-acting element involved inlow-temperature responsiveness
EIRE 1367 + TTCGACC Elicitor-responsive element
P-box 1110 - CCTTTTG Gibberellin-responsive element
AT1-motif 612 + ATTAATTTTACA Light responsive element
Box 4 1489
612
907
+
-
+
ATTAAT Light responsive element
Gap-box 935 + AAATGGAGA Light responsive element
G-Box 842
202
1405
+
-
+
CACGT(G/T)/GACATGTGGT Light responsive element
GT1-motif 894 - GGTTAA Light responsive element
I-box 1252 - CTCTTATGCT Light responsive element
L-box 794 + AAATTAACCAAC Light responsive element
MNF1 401 - GTGCCC(A/T)
(A/T)
Light responsive element
Sp1 879
876
-
-
CC(G/A)CCC Light responsive element
TCT-motif 433 + TCTTAC Light responsive element
MYB-
CORE
488 - CCGTTG MYB-binding site
991 - tAACCGct MYB-binding site
1517 + TAACCG MYB-binding site

注:+表示正链,-代表示负链。

Note: + represents plus strand, - represents minus strand.

2.2 LcUFGT启动子的克隆及顺式作用元件分析

基于荔枝基因组信息,利用特异引物经过PCR扩增获得LcUFGT1启动子序列并测序,得到的启动子序列长度为1584 bp。分析发现LcUFGT1启动子上有3个MYB-CORE位点。另外还发现了一些与环境与激素响应元件,比如光响应元件(AE-box,ATCT-motif,Box 4,Box I,CATT-motif,G-box,I-box等),温度响应元件(LTR),赤霉素响应元件(P-box),茉莉酸响应元件(CGTCA-motif),水杨酸响应元件(TCA- element)等,具体的位置和序列信息见表3
表3 LcUFGT1启动子预测的顺式作用元件

Tab. 3 Predicted cis-elements in promoter of LcUFGT1

顺式作用
元件
Site Name
位置
Position

Strand
序列(5′-3′)
Sequence (5′-3′)
预测的功能
Function
5′ UTR Py-
rich stretch
376
232
263
+
-
-
TTTCTTCTCT cis-acting element conferring high transcription levels
AE-box 347 + AGAAACAT Light responsive element
ARE 256
198
-
+
TGGTTT Cis-acting regulatory element essential for the anaerobic induction
ATCT-motif 1182
731
-
+
AATCTAATCT Light responsive element
Box 4 1442
309
+
-
ATTAAT Light responsive element
Box I 1194
413
479
291
-
-
-
-
TTTCAAA light responsive element
CATT-
motif
958 - GCATTC Light responsive element
CGTCA-
motif
330 - CGTCA Cis-acting regulatory element involved in the MeJA-responsiveness
ELI-box3 201 - AAACCAATT Elicitor-responsive element
ERE 413 - ATTTCAAA Ethylene-responsive element
G-box 562 + GCCTTGTGTAG Light responsive element
GA-motif 234 + ATAGATAA Light responsive element
GATA-
motif
731 - AAGATAAGATT Light responsive element
GT1-motif 101 + GGTTAA Light responsive element
I-box 1381
731
1206
729
-
-
+
-
cCATATCCAAT
GATAAGATT
atGATAAGGTC
aAGATAAGA
Light responsive element
LTR
LTR
1418
666
-
-
CCGAAA
CCGAAA
Cis-acting element involved in low-temperature responsiveness
MNF1 1395 + GTGCCC
(A/T)(A/T)
Light responsive element
P-box 1197 + CCTTTTG Gibberellin-responsive element
TCA-
element
147 - GAGAAGAATA Cis-acting element involved in salicylic acid responsiveness
TCT-motif 724 + TCTTAC Light responsive element
757 + CAACCG MYB-binding site
MYB-
CORE
363 - GCCGTTATAT MYB-binding site
85 - GCCAAC MYB-binding site

注:+表示正链,-代表示负链。

Note: + represents plus strand, - represents minus strand.

2.3 LcMYB1结合LcDFRLcUFGT1启动子区域的分析

本研究采用双荧光报告基因的检测方法研究LcMYB1转录因子和LcDFRLcUFGT1启动子片段的结合区域。如图1所示,当LcDFR启动子从5′ 端开始减少到929 bp时,LcMYB1激活这段启动子的活力下降约70%,说明删减的这段区域(上游904 bp至1425 bp)内含有LcMYB1结合的重要顺式作用元件。进一步分析这段序列内的顺式作用元件,发现该段内含有1个MYB-CORE元件。当LcUFGT1启动子删减到上游610 bp时,启动子仍然保持着与1584 bp相同的活力。推测在LcUFGT1启动子的最后一段610 bp内含有LcMYB1重要顺式作用元件,分析发现该段内含有2个MYB-CORE元件,分别位于上游363 bp和上游85 bp处。

2.4 利用酵母单杂交验证LcMYB1结合LcDFRLcUFGT1启动子的区域

将通过双荧光素酶实验验证的部分启动子序列LcDFR(上游904 bp至1425 bp)和LcUFGT(上游610 bp至ATG)连接到pAbAi质粒上得到proLcDER-AbAi和proLcUFGT-AbAi重组质粒,将这2个质粒分别转入Y1H Gold细胞中在不含有AbA的SD/-Ura上固体培养基上生长正常,说明2个启动子均已成功转入到酵母细胞中。当培养基中添加30 mmol/L AbA时,含有proLcDER- AbAi的酵母不能正常生长;当培养基中添加125 mmol/L AbA时,含有proLcUFGT-AbAi的酵母不能正常生长;说明一定浓度的AbA可以抑制启动子的本底活性。进一步将pGADT7-LcMYB1质粒分别转入含有proLcDER-AbAi和proLcUFGT- AbAi的酵母细胞后在不含AbA的SD/-Leu培养基上均能正常生长,说明pGADT7-LcMYB1质粒已经成功转入,且在含有AbA的SD/-Leu培养基上也能正常生长,说明LcMYB1编码的蛋白可以与上述的LcDFRLcUFGT1启动子片段结合(图2)。
图2 酵母单杂交分析LcMYB1转录因子结合LcDFRLcUFGT1启动子片段

Fig. 2 LcMYB1 binds to promoter fragments of LcDFR and LcUFGT1 confirmed by yeast one hybrid assays

3 讨论

在植物的转录调控过程中,启动子上的顺式作用元件起着非常重要作用,反式作用因子通过与顺式作用元件结合调控基因的转录,从而影响特定的基因的时空表达特性及响应外界信号。植物花色苷生物合成是次生代谢途径中研究最为深入的途径之一,转录因子MYB-bHLH-WD40蛋白复合体通过与花色苷生物合成结构基因启动子结合调控其转录[12,13,14]。在烟草中,NtAn2(R2R3- MYB)能与bHLH转录因子形成复合体调控花色苷生物合成结构基因NtCHSNtDFR的启动子,从而调控花色苷的积累[15,16]。矮牵牛中,PhJAF13(bHLH转录因子)和PhAN2(MYB转录因子)互作可以结合到PhDFR基因的启动子上[17]。在亚洲百合中,LhMYB12和LhMYB6能分别与LhbHLH2相互作用激活结构基因LhDFR,LhCHSaLhCHSb的表达[18]。MdMYB1是光调控苹果果皮花色苷积累的关键转录因子,其可以激活花色苷生物合成结构基因MdDFRMdUFGT的表达,杨梅的MrMYB1AtbHLH共同表达时可以促进拟南芥AtDFR的启动子活性增加,MrMYB1与MrbHLH1相互作用可以调控杨梅果实中花色苷生物合成途径中的大多数结构基因[19,20,21]。上述的研究结果说明,MYB转录因子通过结合到结构基因启动子并激活其转录,决定花色苷是否积累和积累多少。在荔枝中,LcMYB1的表达水平与不同组织、不同荔枝品种果皮、同一品种不同发育阶段果皮中花色苷含量正相关,同时关键结构基因LcDFRLcUFGT的表达模式与LcMYB1一致,这说明LcDFRLcUFGT可能是LcMYB1的下游靶基因[5, 7, 10]
MYB转录因子一般结合在启动子的两类顺式作用元件MYB-CORE elements (CNGTTR,也称MBS)和AC-rich elements([A/C]CC[A/T]A [A/C])[9]LcDFRLcUFGT1是荔枝花色苷生物合成的关键结构基因[5, 7]。它们的启动子序列包括有大量的顺式作用元件,其中LcDFRLcUFGT1启动子上分别含有1和3个MYB-CORE元件。本研究通过启动子5′ 端删减的方法,确定了LcMYB1激活LcDFR基因起始密码上游929 bp到1449 bp的启动子区域,该区段仅包含1个MYB- CORE,LcUFGT1基因起始密码到上游617 bp的区域,该区段包含2个MYB-CORE。进一步利用酵母单杂交实验也验证了LcMYB1可以结合到LcDFRLcUFGT1启动子的这部分片段上。在葡萄中,通过酵母单杂交实验发现VvMYBA1也可以结合到VvDFRVvUFGT启动子上,但是具体的区段并没有进一步分析[22]。本论文利用双荧光素酶和酵母单杂实验证明了LcMYB1通过结合到LcDFRLcUFGT1的启动子激活基因表达,从而发挥调控花色苷生物合成的作用,并且利用截短启动子序列的手段缩小了LcMYB1结合到启动子上的区域范围,为进一步的精确定位LcMYB1结合的顺式作用元件奠定良好的基础。
分析还发现在LcDFRLcUFGT启动子上还发现了大量的光响应元件,前期研究发现套袋遮光抑制荔枝果皮花色苷积累,同时LcDFRLcUFGT的转录也显著受抑制,这有可能和它们启动子上的光响应元件有一定的关系[5, 23]。此外,在LcDFRLcUFGT启动子上还发现了一些胁迫响应和激素响应元件,是否这些元件也参与调控转录还需要进一步研究。
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