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Article(id=1218263520702026318, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1218263514121163166, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2017-0499, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1495036800000, receivedDateStr=2017-05-18, revisedDate=1498060800000, revisedDateStr=2017-06-22, acceptedDate=null, acceptedDateStr=null, onlineDate=1768386257577, onlineDateStr=2026-01-14, pubDate=1510416000000, pubDateStr=2017-11-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1768386257577, onlineIssueDateStr=2026-01-14, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1768386257577, creator=13701087609, updateTime=1768386257577, updator=13701087609, issue=Issue{id=1218263514121163166, tenantId=1146029695717560320, journalId=1189982191388893191, year='2017', volume='52', issue='11', pageStart='1639', pageEnd='1776', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1768386256008, creator=13701087609, updateTime=1768386717926, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1218265451596010257, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1218263514121163166, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1218265451596010258, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1218263514121163166, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=1770, endPage=1776, ext={EN=ArticleExt(id=1218263521184371311, articleId=1218263520702026318, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Bioinformatics analysis and expressed level of Auxin response factor genes in Scutellaria baicalensis, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=ORIGINAL ARTICLES, runingTitle=null, highlight=null, articleAbstract=

Auxin response factor (ARF) is an important transcription factor for auxin signal transduction pathway, which regulates virtually every aspect of plant growth and development from embryogenesis to senescence. Nine full-length genes of ARF transcription factors were obtained from transcriptome dataset of Scutellaria baicalensis Georgi using the bioinformatics methods. The nucleotide and protein characteristics, subcellular localization, senior structural domains and conservative forecasts of those ARF transcription factors were analyzed. The phylogenetic tree showed that the nine ARFs in S. baicalensis were clustered together with ARF transcription factors in Arabidopsis thaliana, Oryza sativa subsp. Japonica and Nicotiana attenuate. The results of gene expression showed that:① The expression levels of ARF1, ARF3, ARF4, ARF8, ARF20 and ARF24 were upregulated after 100 μmol·L-1 GA3 treatment. However, the expression levels of ARF6 and ARF18 were downregulated; ② Those ARF genes were mainly expressed in the flowers of S. baicalensis; ③ There was a significant correlation between ARF genes and the genes involved in flavonoid biosynthesis. Our results provide a basis for further understanding the molecular regulation mechanism of flavonoid biosynthesis in S. baicalensis.

, correspAuthors=Juan LIU, Yuan YUAN, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2017 Acta Pharmaceutica Sinica. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Ti-ying CHEN, Juan LIU, Yuan YUAN, Jun-hui ZHOU, Lu-qi HUANG), CN=ArticleExt(id=1218263523872920305, articleId=1218263520702026318, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=黄芩ARF基因家族生物信息学及表达分析, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

ARF转录因子在植物的生长发育中具有重要意义，是生长素信号传导途径中的重要转录因子。该研究通过生物信息学方法，从黄芩转录组中获得9个具有全长的ARF基因，分别对其核苷酸特性、蛋白质理化性质、亚细胞定位、二级结构、系统发育和基因表达情况进行分析。系统进化树结果显示，这9个黄芩的ARF分别与拟南芥、烟草、水稻中的ARF转录因子聚在一起。ARF基因相对表达分析发现：100 μmol·L-1赤霉素处理后，ARF1、ARF3、ARF4、ARF8、ARF20、ARF24表达量升高，ARF6、ARF18表达量降低；ARF基因在黄芩的花中具有较高的表达量；ARF基因与黄芩中黄酮类合成及调控基因的表达具有一定的相关性。本研究为进一步探讨ARF基因在黄芩中黄酮类成分积累的调控机制提供依据。

, correspAuthors=刘娟, 袁媛, authorNote=null, correspAuthorsNote=
* 刘娟, E-mail: ;
袁媛, Tel: 86-10-64014411-2956, E-mail:
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Plant Physiol, 2002, 129:1507-1520., articleTitle=null, refAbstract=null)], funds=[Fund(id=1218968422520635538, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, awardId=81573522, language=CN, fundingSource=国家自然科学基金资助项目(81573522), fundOrder=null, country=null), Fund(id=1218968422654853280, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, awardId=ZZ10-008, language=CN, fundingSource=中央级公益性科研院所基本科研业务费专项资金资助项目(ZZ10-008), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1218968414098473494, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, xref=null, ext=[AuthorCompanyExt(id=1218968414106862106, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, companyId=1218968414098473494, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China), AuthorCompanyExt(id=1218968414115250713, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, companyId=1218968414098473494, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=中国中医科学院中药资源中心, 北京 100700)])], figs=[ArticleFig(id=1218968419077112719, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=EN, label=null, caption=null, figureFileSmall=LxGzXCJiPAgSeGQ4ljGsMA==, figureFileBig=f07462PxcMGoJ34Kqexgaw==, tableContent=null), ArticleFig(id=1218968419190358938, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=CN, label=Figure 1, caption=

Electrophoresis chart of S. baicalensis ARF PCR products. M: DL2000 DNA marker; 1-9: PCR products of ARF1, ARF3, ARF4, ARF6, ARF8, ARF12, ARF18, ARF20 and ARF24

, figureFileSmall=LxGzXCJiPAgSeGQ4ljGsMA==, figureFileBig=f07462PxcMGoJ34Kqexgaw==, tableContent=null), ArticleFig(id=1218968419332965291, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=EN, label=null, caption=null, figureFileSmall=orUN7sVUFlTBngBWcwRmrg==, figureFileBig=5flY+MPSMm89LjSdQGdKEg==, tableContent=null), ArticleFig(id=1218968419462988731, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=CN, label=Figure 2, caption=

Secondary structure predictions of ARF TFs

, figureFileSmall=orUN7sVUFlTBngBWcwRmrg==, figureFileBig=5flY+MPSMm89LjSdQGdKEg==, tableContent=null), ArticleFig(id=1218968420729668551, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=EN, label=null, caption=null, figureFileSmall=pbMSMy3kPpV1Hm4a8qy/+g==, figureFileBig=B9zqOyg5u4Y557ya8v4XDA==, tableContent=null), ArticleFig(id=1218968420905829336, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=CN, label=Figure 3, caption=

Analysis of the phylogenetic relationships of ARF gene members in S. baicalensis, Arabidopsisthaliana, Oryza sativa subsp. Japonica, Vitis vinifera and Nicotiana attenuate. Reddot: S. baicalensis; At: A. thaliana. GenBank Number of AtARFs: At5g20730-NP_568400.2, At1g19220-NP_173356, At1g59750-NP_849830, At5g62000-NM_125438, At2g18390-NP_179430, At2g47170-NP_001324310.1; A4A49: N. attenuate. GenBank Number of NaARFs: A4A49_25919-OIS99983.1, A4A49_26861-OIS98057.1, A4A49_40149-OIT19819.1; VITISV: V vinifera. GenBank Number of VvARFs: VITISV_024151-CAN63853.1, VITISV_030510-CAN80533.1, VITISV_000577-CAN70219.1; Os: O. sativa. GenBank Number of OsARFs: OsARF1-XP_015617187.1, OsARF10-XP_015644138.1, OsARF16-XP_015622435.1

, figureFileSmall=pbMSMy3kPpV1Hm4a8qy/+g==, figureFileBig=B9zqOyg5u4Y557ya8v4XDA==, tableContent=null), ArticleFig(id=1218968421056824295, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=EN, label=null, caption=null, figureFileSmall=MBliAxO5CXsB+d+BR9HUaw==, figureFileBig=caC6jjmOMoMHJqp2hG1T5A==, tableContent=null), ArticleFig(id=1218968421224596472, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=CN, label=Figure 4, caption=

Effect of GA3 treatment on ARF and flavonoids biosynthetic related gene expression in S. baicalensis (n = 3). Expression in 0 h after treatment was set as 1 (*P ≤ 0.05, **P ≤ 0.01)

, figureFileSmall=MBliAxO5CXsB+d+BR9HUaw==, figureFileBig=caC6jjmOMoMHJqp2hG1T5A==, tableContent=null), ArticleFig(id=1218968421409144849, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=EN, label=null, caption=null, figureFileSmall=KjrC6hKU6I65h6FCgAKYbw==, figureFileBig=5et/aP5BdD2tntWtk6sSGQ==, tableContent=null), ArticleFig(id=1218968421547556899, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=CN, label=Figure 5, caption=

The expression levels of ARF and flavonoid biosynthetic related gene expression in S. baicalensis from different organs (n = 3). Expression in the stem was set as 1 (*P ≤ 0.05, **P ≤ 0.01)

, figureFileSmall=KjrC6hKU6I65h6FCgAKYbw==, figureFileBig=5et/aP5BdD2tntWtk6sSGQ==, tableContent=null), ArticleFig(id=1218968421723717686, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Gene nameForward primer sequence (5'-3')Reverse primer sequence (5'-3')Product long/bp
ARF1GGGGCTCCCAAAATAGTGCGTCTGATAACAAACTCAGCAGCATCCGCA746
ARF3GCAGGCTTGTGCGTGACGGAATTTTCCAATTTACAAATTGGTGG828
ARF4TTGGCCGGAGATCCCTTTAGCGCAAAAGGTGAAGACAGCAACATAG762
ARF6GGGAGCAAGCAAAGGATCCAGACCAAGACAATGCTCGTCTGCTCAT1 242
ARF8GGCAATTTCTAAGCGACAAACACAGTGTCCAAAACTCAATGGTTCAAT1 556
ARF12GGGTCCACAATTAATGATGGTAGCTTGGTAAGCTTTCCAATTGGCAA480
ARF18TCCTGCCGCTAGTTTACTGTTTCACGCACCATCCATGCTCACCTTCACAA819
ARF20GTTGGTGTTGAGTCGACAACTCCATTACCATTCTTTCAAGCTTAGTT779
ARF24CATCCCTATACGCACATCGGCGTAAGTTTTCTTAGCACCTAGCCC717
), ArticleFig(id=1218968421853741122, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=CN, label=Table 1, caption=

Sequences of primers used inARF cloning

, figureFileSmall=null, figureFileBig=null, tableContent=
Gene nameForward primer sequence (5'-3')Reverse primer sequence (5'-3')Product long/bp
ARF1GGGGCTCCCAAAATAGTGCGTCTGATAACAAACTCAGCAGCATCCGCA746
ARF3GCAGGCTTGTGCGTGACGGAATTTTCCAATTTACAAATTGGTGG828
ARF4TTGGCCGGAGATCCCTTTAGCGCAAAAGGTGAAGACAGCAACATAG762
ARF6GGGAGCAAGCAAAGGATCCAGACCAAGACAATGCTCGTCTGCTCAT1 242
ARF8GGCAATTTCTAAGCGACAAACACAGTGTCCAAAACTCAATGGTTCAAT1 556
ARF12GGGTCCACAATTAATGATGGTAGCTTGGTAAGCTTTCCAATTGGCAA480
ARF18TCCTGCCGCTAGTTTACTGTTTCACGCACCATCCATGCTCACCTTCACAA819
ARF20GTTGGTGTTGAGTCGACAACTCCATTACCATTCTTTCAAGCTTAGTT779
ARF24CATCCCTATACGCACATCGGCGTAAGTTTTCTTAGCACCTAGCCC717
), ArticleFig(id=1218968422000541777, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Gene nameForward primer sequence (5'-3')Reverse primer sequence (5'-3')Product long/bp
ARF1CAGTTTGGGATGTTGGGGGCGCTGTCTGAGTGAGTGTAGGC262
ARF3TGTGTGGGATGTTGGGGGGCGTTAAGCATGGTTGGGTC165
ARF4CAGTGTAATCAGCCCCACACTTATCCACCACCCAAACCAAC155
ARF6TAGTGTTGGTGATGTTGAGGGCCTGCATAGTGGAGAGGGGTGT197
ARF8GCATGGTATCTGCCACGAACGAAAATGCCAAACCCAAATC257
ARF12AGATCTGGCTCGTAGATTTGGTATTTGCTGGACTTCTTGGGGA178
ARF18CTGGCTTCTCCAACCTCCTTGACCATGTTCTGAATCCCTCC214
ARF20AACGTGGAGTGTGGAGAAGTGGTTCCAAGTTCTGCATACCCT193
ARF24CTCCCAGTCTTCCTCACCTCATCCCTGTCTTCCCAGTTCTCTTT203
PAL1GCGAATAGTGTTCATGATGAGGATCAATGGCTGCCTTTCCAGTT148
PAL2GATTCTGCGTCCAACTCAGTGAGCGTCGGCATTATCCCTG182
PAL3GGCCACCAAGATGATCGACAATGGCCAATCTTGCATTG143
CHSGCAGTCCACTTATGCTGATTACGTGAAGTTGTCGTTCTCCTTC156
MYB2GTAGTCCAAAAGCACTCACCTCCAAAAAAATAAACTAAGCA233
MYB8GATGAAAATCCCAAGAGCAACAGCGTCGTCACTTCCACTATCC174
Sb18SCGTTGACTACGTCCCTGCCCTTGTTCACCTACGGAAACCTTGTTACGAC130
), ArticleFig(id=1218968422105399394, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=CN, label=Table 2, caption=

Real-time PCR primer sequences

, figureFileSmall=null, figureFileBig=null, tableContent=
Gene nameForward primer sequence (5'-3')Reverse primer sequence (5'-3')Product long/bp
ARF1CAGTTTGGGATGTTGGGGGCGCTGTCTGAGTGAGTGTAGGC262
ARF3TGTGTGGGATGTTGGGGGGCGTTAAGCATGGTTGGGTC165
ARF4CAGTGTAATCAGCCCCACACTTATCCACCACCCAAACCAAC155
ARF6TAGTGTTGGTGATGTTGAGGGCCTGCATAGTGGAGAGGGGTGT197
ARF8GCATGGTATCTGCCACGAACGAAAATGCCAAACCCAAATC257
ARF12AGATCTGGCTCGTAGATTTGGTATTTGCTGGACTTCTTGGGGA178
ARF18CTGGCTTCTCCAACCTCCTTGACCATGTTCTGAATCCCTCC214
ARF20AACGTGGAGTGTGGAGAAGTGGTTCCAAGTTCTGCATACCCT193
ARF24CTCCCAGTCTTCCTCACCTCATCCCTGTCTTCCCAGTTCTCTTT203
PAL1GCGAATAGTGTTCATGATGAGGATCAATGGCTGCCTTTCCAGTT148
PAL2GATTCTGCGTCCAACTCAGTGAGCGTCGGCATTATCCCTG182
PAL3GGCCACCAAGATGATCGACAATGGCCAATCTTGCATTG143
CHSGCAGTCCACTTATGCTGATTACGTGAAGTTGTCGTTCTCCTTC156
MYB2GTAGTCCAAAAGCACTCACCTCCAAAAAAATAAACTAAGCA233
MYB8GATGAAAATCCCAAGAGCAACAGCGTCGTCACTTCCACTATCC174
Sb18SCGTTGACTACGTCCCTGCCCTTGTTCACCTACGGAAACCTTGTTACGAC130
), ArticleFig(id=1218968422218645614, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Gene
name		Length
/bp		Full
length cDNA		Molecular
mass/kDa		Amino
acid number		Isoelectric
point
ARF1840Yes20.6931816.43
ARF3908Yes20.9871868.48
ARF4843Yes21.2491855.94
ARF61 242Yes37.1763464.51
ARF81 556Yes34.6793125.30
ARF12531Yes14.5631285.39
ARF18879Yes23.9352266.16
ARF20851Yes18.8071656.15
ARF24777Yes22.9942088.56
), ArticleFig(id=1218968422323503220, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1218263520702026318, language=CN, label=Table 3, caption=

The characteristics of S. baicalensis ARFs

, figureFileSmall=null, figureFileBig=null, tableContent=
Gene
name		Length
/bp		Full
length cDNA		Molecular
mass/kDa		Amino
acid number		Isoelectric
point
ARF1840Yes20.6931816.43
ARF3908Yes20.9871868.48
ARF4843Yes21.2491855.94
ARF61 242Yes37.1763464.51
ARF81 556Yes34.6793125.30
ARF12531Yes14.5631285.39
ARF18879Yes23.9352266.16
ARF20851Yes18.8071656.15
ARF24777Yes22.9942088.56
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黄芩ARF基因家族生物信息学及表达分析
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陈媞颖 , 刘娟 * , 袁媛 * , 周骏辉 , 黄璐琦
药学学报 | 研究论文 2017,52(11): 1770-1776
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药学学报 | 研究论文 2017, 52(11): 1770-1776
黄芩ARF基因家族生物信息学及表达分析
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陈媞颖, 刘娟* , 袁媛* , 周骏辉, 黄璐琦
作者信息
  • 中国中医科学院中药资源中心, 北京 100700

通讯作者:

* 刘娟, E-mail: ;
袁媛, Tel: 86-10-64014411-2956, E-mail:
Bioinformatics analysis and expressed level of Auxin response factor genes in Scutellaria baicalensis
Ti-ying CHEN, Juan LIU* , Yuan YUAN* , Jun-hui ZHOU, Lu-qi HUANG
Affiliations
  • National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
出版时间: 2017-11-12 doi: 10.16438/j.0513-4870.2017-0499
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摘要
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ARF转录因子在植物的生长发育中具有重要意义，是生长素信号传导途径中的重要转录因子。该研究通过生物信息学方法，从黄芩转录组中获得9个具有全长的ARF基因，分别对其核苷酸特性、蛋白质理化性质、亚细胞定位、二级结构、系统发育和基因表达情况进行分析。系统进化树结果显示，这9个黄芩的ARF分别与拟南芥、烟草、水稻中的ARF转录因子聚在一起。ARF基因相对表达分析发现：100 μmol·L-1赤霉素处理后，ARF1、ARF3、ARF4、ARF8、ARF20、ARF24表达量升高，ARF6、ARF18表达量降低；ARF基因在黄芩的花中具有较高的表达量；ARF基因与黄芩中黄酮类合成及调控基因的表达具有一定的相关性。本研究为进一步探讨ARF基因在黄芩中黄酮类成分积累的调控机制提供依据。

黄芩  /  ARF转录因子  /  生物信息学  /  表达分析

Auxin response factor (ARF) is an important transcription factor for auxin signal transduction pathway, which regulates virtually every aspect of plant growth and development from embryogenesis to senescence. Nine full-length genes of ARF transcription factors were obtained from transcriptome dataset of Scutellaria baicalensis Georgi using the bioinformatics methods. The nucleotide and protein characteristics, subcellular localization, senior structural domains and conservative forecasts of those ARF transcription factors were analyzed. The phylogenetic tree showed that the nine ARFs in S. baicalensis were clustered together with ARF transcription factors in Arabidopsis thaliana, Oryza sativa subsp. Japonica and Nicotiana attenuate. The results of gene expression showed that:① The expression levels of ARF1, ARF3, ARF4, ARF8, ARF20 and ARF24 were upregulated after 100 μmol·L-1 GA3 treatment. However, the expression levels of ARF6 and ARF18 were downregulated; ② Those ARF genes were mainly expressed in the flowers of S. baicalensis; ③ There was a significant correlation between ARF genes and the genes involved in flavonoid biosynthesis. Our results provide a basis for further understanding the molecular regulation mechanism of flavonoid biosynthesis in S. baicalensis.

Scutellaria baicalensis  /  ARF transcription factor  /  bioinformatics  /  expression analysis
陈媞颖, 刘娟, 袁媛, 周骏辉, 黄璐琦. 黄芩ARF基因家族生物信息学及表达分析. 药学学报, 2017 , 52 (11) : 1770 -1776 . DOI: 10.16438/j.0513-4870.2017-0499
Ti-ying CHEN, Juan LIU, Yuan YUAN, Jun-hui ZHOU, Lu-qi HUANG. Bioinformatics analysis and expressed level of Auxin response factor genes in Scutellaria baicalensis[J]. Acta Pharmaceutica Sinica, 2017 , 52 (11) : 1770 -1776 . DOI: 10.16438/j.0513-4870.2017-0499
正文
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中药黄芩为临床常用药材, 来源于唇形科多年生草本植物黄芩Scutellaria baicalensis Georgi的干燥根, 其主要活性成分为黄芩苷、黄芩素等黄酮类化合物。研究表明, 高温、光照、缺水等适度的环境胁迫均能促进黄芩活性成分的积累[1-4], 且与植物内源激素赤霉素和生长素的调控密切相关。光照条件下, 悬浮细胞中黄芩苷的含量随生长素IAA (indole-3-acetic acid)含量的降低而降低; 水分胁迫下, 黄芩中黄芩素的含量随着生长素IAA含量的升高而升高, 且外源赤霉素(gibberellin A3, GA3)影响黄芩中内源生长素及活性成分的含量[5-7]。
转录因子在调控苯丙烷类次生代谢产物积累与植物抗逆反应中发挥重要作用, 然而苯丙烷类化合物基因调控网络中转录因子之间的相互作用和协同作用却鲜见报道。前期研究发现, 黄芩中MYB蛋白可以激活类黄酮合成途径下游关键酶基因的表达, 多种转录因子(eg: ARF bHLH等)参与调控过程。ARF (auxin response factor)是一类较新发现的转录因子家族, 对生长素响应基因的表达起到激活或抑制作用, 广泛参与调控生长素及其他植物激素信号转导途径[8]。同时, ARF转录因子参与植物多途径信号的协同作用, 如番茄中的SlARF7基因是生长素和赤霉素信号途径的关键结合位点[9], 拟南芥中的MYB77转录因子通过与ARF7协同作用, 控制环境变化对于侧根生长发育的影响[10]。
近年来, 对于ARF转录因子的功能研究逐渐增多, 主要集中在拟南芥、烟草、水稻、丹参等植物中[11-13], 黄芩中ARF转录因子的功能及理化性质却未见报道。本文通过黄芩ARF转录因子的生物信息学分析, 同时比较ARF与黄芩次生代谢产物合成相关基因的表达, 为进一步研究黄芩中ARF转录因子的生物学功能奠定基础, 为完善黄芩中黄酮类成分的分子调控网络提供依据。
材料与方法
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材料
黄芩种子为中国中医科学院中药资源中心实验室保存, 将黄芩种子于湿润的滤纸上萌发, 萌发苗两周后移栽至花盆中, 25 ℃、16 h光照室温条件下培养。以100 μmol·L-1 GA3喷施黄芩叶片, 并分别于喷施后的0、1、2、3 h取样, -80 ℃冰箱保存备用。夏季黄芩花期时, 于同一植株不同部位分别取花、根、茎、叶, 清水清洗后以滤纸除去多余水分, -80 ℃冰箱保存备用。
黄芩ARF基因序列获取
从TAIR数据库中下载拟南芥ARF核酸序列, 以此作为探针, 通过BLAST比对, 在黄芩转录组数据库中搜寻同源序列, 识别标准为e≤10-15, Score≥100, 匹配数b = 1。
生物信息学分析
通过ORF Finder在线工具(http://www.ncbi.nlm.nih.gov/projects/gorf/)预测ARF基因序列的开放阅读框序列。运用在线软件Protparam (expasy.ch/tools/protparam.html)预测ARF编码蛋白的理化性质; 采用ExPASyPROSITE (http://www.expasy.ch/prosite)和CDD (http://www.ncbi.mlm.nih.gov/Structure/cdd/wrpsb.cgi)进行蛋白质结构域分析; 使用WOLF PSORT (http://wolfpsort.org/)进行蛋白质亚细胞定位信号的预测; 使用SignalP 4.1 Server (http:www.cbs.dtu.dk/services/SignalP)进行分泌蛋白的预测; 使用CFSSP (http://swissmodel.expasy.org/)进行蛋白质二级结构的分析; 使用MEGA 5.0构建系统进化树(Neighbor-joining tree, NJ tree) (bootstrap值设为1 000)。
RNA提取和cDNA合成
样品总RNA采用植物总RNA提取试剂盒(TIANGEN公司)提取, 经1%琼脂糖凝胶电泳检测确定RNA完整性后, 用核酸定量仪测定RNA浓度, 按照cDNA合成试剂盒(TaKaRa公司)说明书进行反转录。
基因克隆
在黄芩ARF基因序列的基础上设计PCR引物, 由生工生物工程(北京)有限公司合成, 见表 1。反应体系按照Trans Start® Fast Pfu DNA Polymerase高保真酶(全式金公司)说明书配制, 50 μL反应体系, 包括5×Trans Start® Fast Pfu Buffer 10 μL、dNTP 4 μL、正反向引物各1 μL、Trans Start® Fast Pfu DNA Polymerase高保真酶1 μL、cDNA模板1μL和ddH2O 32 μL。反应程序为95 ℃预变性1 min; 95 ℃变性20 s, 55 ℃退火20 s, 72 ℃延伸1 min, 40个循环; 72 ℃复性5 min。
Real-time荧光定量PCR
依照黄芩ARF序列设计Real-time荧光定量PCR引物, 扩增产物长度在100~250 bp之间, 由生工生物工程(北京)有限公司合成, 见表 2。反应体系按照SYBR Premix Ex TaqTM Kit (TaKaRa公司)说明书配制, 10 μL反应体系, 包括正反向引物各0.5 μL、SYBR Premix Ex Taq 5μL、cDNA模板1 μL、ddH2O 3 μL。每个反应重复3次(包括阴性对照), 在Light Cycler 480 Ⅱ型实时荧光定量PCR仪(Roche公司)上进行, 结束后进行熔解曲线分析, 扩增程序如下: 94 ℃预变性2 min; 94 ℃变性5 s, 60 ℃退火延伸34 s (每次循环后采集荧光信号), 40个循环; 94 ℃变性10 s, 65~95 ℃做熔解曲线分析, 每个温度以每步0.5 ℃上升, 停留5 s, 获得每个基因的Ct值进行相对定量分析。
基因相对表达量的计算
100 μmol·L-1 GA3处理下黄芩基因表达量的计算是以0 h作为参比基准, 计算不同基因在GA3处理下相对表达量的变化; 不同部位黄芩基因表达量的计算是以茎作为基准参比部位。各基因表达量以内参基因Sb18S作为标准进行相对定量[14], 目的基因表达量采用2-ΔΔCt法计算, 计算公式为2-ΔΔCt = 2-[(Ct目的基因-Ct管家基因)待测组-(Ct目的基因-Ct管家基因)对照组]。
基因表达相关性分析
利用SPSS 23.0软件对黄芩ARF基因及与黄芩黄酮类合成相关基因的表达进行Pearson相关性分析, |r|＞0.7说明两者呈现高度线性相关, 0.7≥|r|≥0.5说明两者呈现中度线性相关, 0.5≥|r|≥0.3则两者呈现低度相关, |r|＜0.3两者相关性极低, P≤0.05为显著水平, P≤0.01为极显著水平[15]。
结果
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1 黄芩ARF转录因子特性分析
通过BLAST比对并对所得基因片段进行拼接, 从黄芩转录组中共得到24个ARF基因序列。ORF Finder预测表明, ARF1、ARF3、ARF4、ARF6、ARF8、ARF12、ARF18、ARF20、ARF24为全长cDNA, 其余基因读码框均不完整, 对全长基因进行克隆并测序验证, 产物电泳图如图 1所示。使用ProtParam预测具有全长cDNA的9个黄芩ARF转录因子的理化性质, 结果如表 3所示。使用CDD数据库分析结构域, 结果表明ARF1、ARF3、ARF4、ARF6、ARF8、ARF12、ARF18、ARF20、ARF24均具有ARF家族所特有的Aux-IAA结构域。
使用WOLF PSORT对黄芩含有全长cDNA的9个转录因子进行蛋白质亚细胞定位的信号预测, 结果表明, ARF4、ARF8、ARF18、ARF24被定位至细胞核中, ARF1定位于线粒体和细胞核中, ARF3定位于细胞质、叶绿体及细胞核中, ARF6定位于线粒体、细胞质及细胞核中, ARF12定位于叶绿体和线粒体中, ARF20定位于细胞核及细胞质中。SignalP 4.1 Server软件分析表明, 黄芩含有全长cDNA的9个ARF转录因子均为非分泌蛋白。
2 黄芩ARF转录因子二级结构分析
使用CFSSP软件对黄芩中含有全长cDNA的9个黄芩ARF转录因子进行二级结构预测, α-螺旋(H)、β-折叠(E)、β-转角(T)所占比例如图 2所示。对于大部分黄芩ARF转录因子而言, α-螺旋在二级结构中所占比例最高, β-转角所占比例相对较低, 但ARF20中β-折叠在二级解构中所占比例最高, 同时α-螺旋也占有很高比例, β-转角所占比例仍旧较低。
3 系统进化树分析
选取黄芩中具全长cDNA的9个ARF转录因子氨基酸序列与拟南芥、烟草、水稻和葡萄中的ARF转录因子序列, 使用MEGA5.0 Neighbor-joining法构建黄芩ARF转录因子系统进化树, 见图 3。系统进化树结果表明, 黄芩中的ARF8、ARF12与拟南芥中的At5g20730、At1g19220及烟草中的A4A49_25919、水稻中的OsARF1、OsARF16等聚为一支, 可能作为转录激活因子参与调控生长素应答基因的表达及促进根系发育[16]; 黄芩中的ARF20与烟草中的A4A49_ 40149聚为一支, 可能与生长素信号通路的激活有关[17]; 黄芩中的ARF1、ARF3、ARF4、ARF6、ARF18、ARF24与拟南芥中的At2g18390、At2g47170聚为一支, 可能与植物种子的发育与蛋白质的运输有关[18, 19]。
4 基因表达分析
为了进一步了解黄芩ARF基因的表达模式和表达水平, 通过Realtime-PCR分别分析了含全长cDNA的9个黄芩ARF基因以及与黄芩黄酮类合成相关的CHS、PAL1、PAL2、PAL3、MYB2和MYB8基因在100 μmol·L-1 GA3处理下0、1、2和3 h的表达量, 以及比较其在根、茎、叶和花4个部位之间表达量的差异。
100 μmol·L-1 GA3处理下, ARF1、ARF3、ARF4、ARF12和PAL2基因表达量在处理后1 h显著升高, ARF6、ARF18和CHS在处理后表达量首先下降, 3 h后又逐渐升高, ARF8和ARF20处理后1 h表达量升高, 随后又逐渐降低, 3 h后表达量再次升高, 见图 4。经简单相关及偏相关分析后发现100 μmol·L-1 GA3处理下, ARF3、ARF12和PAL2相对表达水平呈显著正相关(r = 0.900 6、0.910 8); ARF20与PAL1相对表达水平显著负相关(r = -0.853 6)。
黄芩中含完整读码框的9个ARF转录因子在花、茎、叶和根4个部位中的表达量差异明显, 由图 5可见, 黄芩大部分相关基因在花中均有最高的表达量, 高于茎和叶中的表达量。经简单相关及偏相关分析后发现ARF1、ARF3、ARF4、ARF6、ARF12、ARF18和ARF24均与PAL1在黄芩不同部位中相对表达水平显著正相关(r = 0.929 1、0.817 5、0.998 7、0.983 0、0.936 2、0.849 8、0.978 9)。
讨论
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ARF转录因子是一类较新发现的转录因子家族, 广泛参与植物体内生长素等激素信号传导途径。本项目组前期研究证明, 温度、光照、缺水等适度环境胁迫能够增加黄芩有效成分的积累, 且黄芩活性成分的积累与PAL、CHS等关键酶基因有关。本文基于已获得的黄芩cDNA文库序列, 用生物信息学的方法结合基因表达分析, 研究黄芩中ARF转录因子的功能及与类黄酮物质合成相关基因之间的关系。本文共获得了9个含全长cDNA的ARF基因, 分别命名为ARF1、ARF3、ARF4、ARF6、ARF8、ARF12、ARF18、ARF20和ARF24。基因表达分析结果表明, 黄芩中ARF基因与黄酮次生代谢相关基因PAL关系密切, 苯丙氨酸解氨酶(PAL)能够催化苯丙烷类代谢第1步反应, 是黄芩苷合成途径中的关键酶[20]。GA3处理条件下, 黄芩中ARF3、ARF12基因与PAL2基因在表达水平上显示出较强的协同性, 据此推测黄芩中ARF基因可能参与调控黄酮类化合物的次生代谢。系统进化树结果显示, 黄芩中的ARF12与拟南芥中的At5g20730、At1g19220等聚为一支, At5g20730、At1g19220在拟南芥中参与激活生长素应答反应与促进根系发育[21], 且生长素在黄芩中参与调控黄芩素和黄芩苷的积累, 由此推断ARF12可能参与调控黄芩中的生长素信号通路, 进而影响黄芩中活性成分的积累。本文研究结果为进一步了解转录因子调控黄芩活性成分生物合成分子机制奠定基础, 并为完善黄芩中黄酮类活性成分分子调控网络提供了依据。
基金
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  • 国家自然科学基金资助项目(81573522)
  • 中央级公益性科研院所基本科研业务费专项资金资助项目(ZZ10-008)
文献
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参考文献 引证文献
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2017年第52卷第11期
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doi: 10.16438/j.0513-4870.2017-0499
  • 接收时间：2017-05-18
  • 首发时间：2026-01-14
  • 出版时间：2017-11-12
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  • 收稿日期：2017-05-18
  • 修回日期：2017-06-22
基金
国家自然科学基金资助项目(81573522)
中央级公益性科研院所基本科研业务费专项资金资助项目(ZZ10-008)
作者信息
    中国中医科学院中药资源中心, 北京 100700

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* 刘娟, E-mail: ;
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Number of
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Number of
species		 占总种数比例
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total species (%)		 属
Genus		 种数
Number of
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鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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