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Article(id=1276862290477585142, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276862113658303045, articleNumber=null, orderNo=null, doi=10.3969/j.issn.1000-2561.2025.03.004, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1729440000000, receivedDateStr=2024-10-21, revisedDate=null, revisedDateStr=null, acceptedDate=1730908800000, acceptedDateStr=2024-11-07, onlineDate=1782357293003, onlineDateStr=2026-06-25, pubDate=1742832000000, pubDateStr=2025-03-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1782357293003, onlineIssueDateStr=2026-06-25, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1782357293003, creator=13701087609, updateTime=1782357293003, updator=13701087609, issue=Issue{id=1276862113658303045, tenantId=1146029695717560320, journalId=1235980609244409860, year='2025', volume='46', issue='3', pageStart='515', pageEnd='775', issueExtLink='null', onlineDate='null', pubDate='1742832000000', pubDateStr='2025-03-25', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1782357250847, creator='13701087609', updateTime=1782357480466, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1276863076821496476, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276862113658303045, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1276863076825690781, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276862113658303045, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=544, endPage=552, ext={EN=ArticleExt(id=1276862290800546552, articleId=1276862290477585142, tenantId=1146029695717560320, journalId=1235980609244409860, language=EN, title=Cloning and Expression Analysis of vfmE gene from Soft Rot Pathogen Dickeya fangzhongdai Onc5 of Oncidium, columnId=1236256430337085821, journalTitle=Chinese Journal of Tropical Crops, columnName=Omics & Biotechnology, runingTitle=null, highlight=null, articleAbstract=

Dickeya fangzhongdai is one of the main pathogens causing the devastating disease (soft rot disease) of Orchidaceae. Pathogenic genes play a crucial role in the infection process. Dickeya fangzhongdai Onc5 was isolated from the diseased plant (Oncidium, Gower Ramsey) in Fujian province. Pathogenic gene play an important role in the interaction between pathogens and plants. The purpose of this study was to larify the molecular biological characteristics of D. fangzhongdai Onc5 vfmE gene and analysis its role in the infection process, so as to provide theretical basis for further reveal the pathogenic mechanism of D. fangzhongdai Onc5 vfmE gene in the infection process. Using the D. fangzhongdai Onc5 DNA as template, of vfmE gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) and its bioinformatics were analyzed. The expression of vfmE gene was analyzed during D. fangzhongdai Onc5 infecting Oncidium by quantitative reverse transcription PCR (RT-qPCR). The result showed that the ORF sequence of vfmE gene was 564 bp, encoding 187 amino acids with a molecular weight of 21.93 kDa and isoelectric point of 9.01 and a conserved AraC-superfamily domain. The vfmE protein was an unstable hydrophilic protein without signal peptide and transmembrane structure. The secondary structure of protein was mainly composed of α-helix (58.29%) and random coil (40.64%). Sequence similarity analysis revealed that the translated molecules showed high homology with other pathogens in the genus Dickeya (>86%). RT-qPCR analysis showed that vfmE gene was highly expressed continuously throughout the infection process of D. fangzhongdai Onc5, and the highest expression level was at 12 h. vfmE protein plays an important role in the infection of D. fangzhongdai Onc5. Research on the pathogeneisis-related gene vfmE in D. fangzhongdai Onc5 provide a theoretical basis for further research on the vfmE gene function and pathogenic regulation mechanism in Dickeya genus. Furthermore, such studies may be useful for finding new target to control plant soft rot disease.

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狄克氏菌（Dickeya fangzhongdai）是引起兰科植物毁灭性病害软腐病（soft rot disease）的主要病原菌之一。病原菌致病基因在病原菌与植物互作中发挥至关重要的作用。软腐病菌D. fangzhongdai Onc5从福建南茜文心兰（Oncidium，Gower Ramsey）软腐病患病植株中分离而来。本研究旨在明确D. fangzhongdai Onc5 vfmE基因的分子生物学特征，并分析其在侵染寄主过程中的作用，为揭示vfmE基因在D. fangzhongdai Onc5侵染寄主过程中的致病机制提供理论依据。本研究以D. fangzhongdai Onc5基因组DNA为模版，通过RT-PCR扩增，成功获得vfmE基因，并进行生物信息学分析；利用RT-qPCR分析vfmE基因在D. fangzhongdai Onc5侵染文心兰过程中的表达情况。结果表明：D. fangzhongdai Onc5 vfmE基因的ORF为564 bp，编码187个氨基酸；vfmE蛋白质的分子质量为21.93 kDa，理论等电点（pI）为9.01，含1个AraC超家族结构域；vfmE蛋白质为结构不稳定的亲水性蛋白，无信号肽，不存在跨膜结构域；其蛋白质二级结构主要为α-螺旋（58.29%）和无规则卷曲（40.64%）；同源性分析表明，其氨基酸序列与Dickeya属其他菌种的vfmE序列具有很高的相似性（>86%）；RT-qPCR分析表明：vfmE基因在D. fangzhongdai Onc5侵染文心兰叶片和假鳞茎后均持续高表达，在12 h的表达量最高（P<0.01），表明vfmE蛋白在D. fangzhongdai Onc5侵染文心兰的过程中发挥着重要的作用。本研究结果为进一步研究vfmE基因功能和Dickeya属病原菌致病机制提供提论基础，同时也有利于发展植物软腐病新的防治靶标。

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王文婷（1992—），女，博士，副教授，研究方向：植物天然产物活性与植物病理。

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* 卢秋巍（LU Qiuwei），E-mail：。
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王文婷（1992—），女，博士，副教授，研究方向：植物天然产物活性与植物病理。

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王文婷（1992—），女，博士，副教授，研究方向：植物天然产物活性与植物病理。

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Frontiers in Immunology, 2023, 14: 1191209., articleTitle=Unveiling a virulence-regulating mechanism in Aeromonas hydrophila: a quantitative exoproteomic analysis of an AraC-like protein, refAbstract=null), Reference(id=1276862312283771744, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276862290477585142, doi=null, pmid=null, pmcid=null, year=2022, volume=132, issue=2, pageStart=1319, pageEnd=1329, url=null, language=null, rfNumber=[21], rfOrder=30, authorNames=SAHEBI M, TARIGHI S, TAHERI P, journalName=Journal of Applied Microbiology, refType=null, unstructuredReference=SAHEBI M, TARIGHI S, TAHERI P. The Arac - like transcriptional regulator YqhC is involved in pathogenicity of Erwinia amylovora[J]. 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M: DL2000 DNA marker.

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A：vfmE蛋白质二级结构（蓝色字母：α-螺旋；黄色字母：无规则卷曲；红色字母：延伸链）；B：vfmE蛋白质三级结构；C：vfmE蛋白互作网络关系。

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不同小写字母表示差异显著（P<0.01）。

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Primers used in this study

, figureFileSmall=null, figureFileBig=null, tableContent=
引物名称Primer name引物序列（5′-3′）Primer sequence (5′-3′)功能Function
vfmE-FATGAGCTTACAGAACACCTACG扩增
vfmE-RTTAATTACAGAGGTTCTGGATATTATC
recA-FCAATCGGTCAAGGCAAGGCTAACG
recA-RACACTCGGCACGGCTTCATTATC
E-FAACTGGTCGCTCACCGATATTTGC荧光定量
E-RCGGCGGAATGTTGTAGGTCTTGG
), ArticleFig(id=1276862307930084159, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276862290477585142, language=CN, label=表1, caption=

本研究所用引物

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引物名称Primer name引物序列（5′-3′）Primer sequence (5′-3′)功能Function
vfmE-FATGAGCTTACAGAACACCTACG扩增
vfmE-RTTAATTACAGAGGTTCTGGATATTATC
recA-FCAATCGGTCAAGGCAAGGCTAACG
recA-RACACTCGGCACGGCTTCATTATC
E-FAACTGGTCGCTCACCGATATTTGC荧光定量
E-RCGGCGGAATGTTGTAGGTCTTGG
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文心兰软腐病菌Dickeya fangzhongdai Onc5 vfmE基因的克隆及表达分析
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王文婷 , 任驰 , 丁建华 , 荆恩荣 , 卢秋巍 *
热带作物学报 | 组学与生物技术 2025,46(3): 544-552
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热带作物学报 |组学与生物技术 2025 , 46 (3) : 544 -552
文心兰软腐病菌Dickeya fangzhongdai Onc5 vfmE基因的克隆及表达分析
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王文婷, 任驰, 丁建华, 荆恩荣, 卢秋巍*
作者信息
  • 忻州师范学院生物系，山西忻州　034000
通讯作者:
* 卢秋巍（LU Qiuwei），E-mail：。
Cloning and Expression Analysis of vfmE gene from Soft Rot Pathogen Dickeya fangzhongdai Onc5 of Oncidium
Wenting WANG, Chi REN, Jianhua DING, Enrong JING, Qiuwei LU*
Affiliations
  • Department of Biology, Xinzhou Normal University, Xinzhou, Shanxi 034000, China
出版时间: 2025-03-25 doi: 10.3969/j.issn.1000-2561.2025.03.004
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狄克氏菌（Dickeya fangzhongdai）是引起兰科植物毁灭性病害软腐病（soft rot disease）的主要病原菌之一。病原菌致病基因在病原菌与植物互作中发挥至关重要的作用。软腐病菌D. fangzhongdai Onc5从福建南茜文心兰（Oncidium，Gower Ramsey）软腐病患病植株中分离而来。本研究旨在明确D. fangzhongdai Onc5 vfmE基因的分子生物学特征，并分析其在侵染寄主过程中的作用，为揭示vfmE基因在D. fangzhongdai Onc5侵染寄主过程中的致病机制提供理论依据。本研究以D. fangzhongdai Onc5基因组DNA为模版，通过RT-PCR扩增，成功获得vfmE基因，并进行生物信息学分析；利用RT-qPCR分析vfmE基因在D. fangzhongdai Onc5侵染文心兰过程中的表达情况。结果表明：D. fangzhongdai Onc5 vfmE基因的ORF为564 bp，编码187个氨基酸；vfmE蛋白质的分子质量为21.93 kDa，理论等电点（pI）为9.01，含1个AraC超家族结构域；vfmE蛋白质为结构不稳定的亲水性蛋白，无信号肽，不存在跨膜结构域；其蛋白质二级结构主要为α-螺旋（58.29%）和无规则卷曲（40.64%）；同源性分析表明，其氨基酸序列与Dickeya属其他菌种的vfmE序列具有很高的相似性（>86%）；RT-qPCR分析表明：vfmE基因在D. fangzhongdai Onc5侵染文心兰叶片和假鳞茎后均持续高表达，在12 h的表达量最高（P<0.01），表明vfmE蛋白在D. fangzhongdai Onc5侵染文心兰的过程中发挥着重要的作用。本研究结果为进一步研究vfmE基因功能和Dickeya属病原菌致病机制提供提论基础，同时也有利于发展植物软腐病新的防治靶标。

狄克氏菌  /  vfmE基因  /  克隆  /  生物信息学分析  /  表达分析

Dickeya fangzhongdai is one of the main pathogens causing the devastating disease (soft rot disease) of Orchidaceae. Pathogenic genes play a crucial role in the infection process. Dickeya fangzhongdai Onc5 was isolated from the diseased plant (Oncidium, Gower Ramsey) in Fujian province. Pathogenic gene play an important role in the interaction between pathogens and plants. The purpose of this study was to larify the molecular biological characteristics of D. fangzhongdai Onc5 vfmE gene and analysis its role in the infection process, so as to provide theretical basis for further reveal the pathogenic mechanism of D. fangzhongdai Onc5 vfmE gene in the infection process. Using the D. fangzhongdai Onc5 DNA as template, of vfmE gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) and its bioinformatics were analyzed. The expression of vfmE gene was analyzed during D. fangzhongdai Onc5 infecting Oncidium by quantitative reverse transcription PCR (RT-qPCR). The result showed that the ORF sequence of vfmE gene was 564 bp, encoding 187 amino acids with a molecular weight of 21.93 kDa and isoelectric point of 9.01 and a conserved AraC-superfamily domain. The vfmE protein was an unstable hydrophilic protein without signal peptide and transmembrane structure. The secondary structure of protein was mainly composed of α-helix (58.29%) and random coil (40.64%). Sequence similarity analysis revealed that the translated molecules showed high homology with other pathogens in the genus Dickeya (>86%). RT-qPCR analysis showed that vfmE gene was highly expressed continuously throughout the infection process of D. fangzhongdai Onc5, and the highest expression level was at 12 h. vfmE protein plays an important role in the infection of D. fangzhongdai Onc5. Research on the pathogeneisis-related gene vfmE in D. fangzhongdai Onc5 provide a theoretical basis for further research on the vfmE gene function and pathogenic regulation mechanism in Dickeya genus. Furthermore, such studies may be useful for finding new target to control plant soft rot disease.

Dickeya fangzhongdai Onc5  /  vfmE gene  /  cloning  /  bioinformatics analysis  /  expression analysis
王文婷, 任驰, 丁建华, 荆恩荣, 卢秋巍. 文心兰软腐病菌Dickeya fangzhongdai Onc5 vfmE基因的克隆及表达分析. 热带作物学报, 2025 , 46 (3) : 544 -552 . DOI: 10.3969/j.issn.1000-2561.2025.03.004
Wenting WANG, Chi REN, Jianhua DING, Enrong JING, Qiuwei LU. Cloning and Expression Analysis of vfmE gene from Soft Rot Pathogen Dickeya fangzhongdai Onc5 of Oncidium[J]. Chinese Journal of Tropical Crops, 2025 , 46 (3) : 544 -552 . DOI: 10.3969/j.issn.1000-2561.2025.03.004
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文心兰（Oncidium）属于兰科文心兰属植物，其植株轻巧，花形优美，花色艳丽，具有较高的观赏价值和商业价值，是世界上最重要的切花和盆花之一。近年来，中国尤其是台湾省文心兰种植面积和产量也在逐年上升，但文心兰切花高峰期正值高温高湿季节，易受到病原菌的侵害引起软腐病。软腐病是文心兰栽培生产最致命的病害之一，感病后植株迅速水渍化，常引起整株植株腐烂致死，进而影响文心兰全产业链的发展[1]。
软腐病菌Dickeya fangzhongdai Onc5从福建南茜文心兰（Oncidium，Gower Ramsey）软腐病患病植株中分离而来，其基因组已测序完成。体外侵染实验证实该菌株还可侵染蝴蝶兰、金线莲及铁皮石斛等其他兰科植物[2]。Dickeya属病原菌主要通过合成和分泌大量植物细胞壁降解酶（plant cell wall degration enzymes, PCWDEs）侵染宿主植物，使其展现“软腐”症状[3]。Dickeya属病原菌寄主范围较广，可引起多种作物和花卉的细菌性软腐病，造成巨大的经济损失。花卉宿主包括菊花、蝴蝶兰、百合、杜鹃、海棠和向日葵等，其他宿主主要涉及土豆、水稻、香蕉、番茄、玉米、菠萝、大米、胡萝卜、梨树和烟草等[4]，尤其近年来由D. zeae引起的水稻细菌性基腐病和香蕉软腐病[5]，以及由D. solani引起的马铃薯软腐病均造成重大的农业损失[6]，因此，关于Dickeya属病原菌致病机理的研究是当前的研究热点。
群体感应（quorum sensing, QS）是一种细菌细胞之间的通信机制，通过释放与细胞密度相关的QS信号分子来调节特定基因的表达，调节细菌的群体行为，涉及细菌毒力和感染寄主[7]。2013年，NASSER等[8]在D. dadantii 3937菌株中发现一种新的群体感应系统——vfm基因簇，该基因簇仅在Dickeya属中被发现且高度保守，该QS系统含有vfmAZBCD，vfmKLMNOPQRSTUVW，vfmFGHIJ三个操纵子和关键调控基因vfmE。操纵子vfmAZBCD和vfmKLMNOPQRSTUVW主要参与信号分子VFM的合成，随后通过ABC转运蛋白vfmFG输出胞外。胞外信号VFM随着细胞数量的增加逐渐积累，当VFM达到一定的阈值，引发双组分系统vfmH/vfmI间的磷酸化，被激活的vfmH诱导vfmE表达，vfmE可进一步激活下游PCWDEs相关基因的表达，影响D. dadantii 3937对寄主的侵染。此外，vfmE也可激活vfmKLMNOPQRSTUVW、vfmFGHIJ和vfmAZBCD，由此，在分子水平上增加了VFM信号合成相关基因的转录样本，实现了VFM信号的快速积累（图1）。与野生型菌株相比，D. dadantii 3937 ΔvfmE突变体对非洲紫罗兰（Saintpaulia ionantha）的致病性明显减弱。2019年，LV等[9]在D. zeae EC1菌株中也发现了D. dadantii 3937同源vfm基因簇，该项研究表明：ΔvfmE突变体中zeamines（D. zeae EC1分泌的一种抗生素类植物毒素）生物合成相关基因（zmsK、zmsA、zmsC和zmsD）以及PCWDEs合成相关基因的表达量均显著降低。此外，该菌株vfm群体感应系统还能够影响T1SS（type Ⅰ secretion systems）、T2SS、T3SS和T4SS分泌系统基因的表达以及病原菌的运动性（motility）。BANERJEE等[10]研究表明，D. dadantii的毒力与第二信使环二鸟甘酸（cyclic-di-GMP，c-di-GMP）有关，当环境中c-di-GMP浓度较低时，vfmE可作为效应蛋白与c-di-GMP结合激活果胶酶（pectate lyase, Pel）合成基因pel的表达。目前，vfmE基因仅在D. dadantii 3937和D. zeae EC1菌株中报道，且都与病原菌致病系统——新型群体感应系统的调控相关。现有研究表明，因菌种间的差异，新型群体感应系统vfm基因簇对致病因子的调控有所不同，或许与vfmE基因功能的差异有关。
在前期的研究中，本课题组在D. fangzhongdai Onc5菌株基因组中发现了D. dadantii 3937同源vfm基因簇，大小约为25 kb，其中包括vfmE。此外，课题组还对vfm基因簇中的关键调控基因vfmH和vfmI进行了克隆、原核表达和蛋白纯化。基于此，本研究以D. fangzhongdai Onc5菌株为研究对象，从其基因组中克隆vfmE基因，并对其生物信息学特征及表达特征进行分析，以期为后续揭示vfmE基因对Dickeya属病原菌致病性的调控机制提供理论参考。
1　材料与方法
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1.1　材料
1.1.1　菌株、质粒及菌株活化
软腐病菌D. fangzhongdai Onc5菌株保存于忻州师范学院生化实验室，将其置于30%的甘油中，于-80 ℃冰箱保存。pUCm-T载体、大肠杆菌DH5α感受态均购自生工生物工程（上海）股份有限公司。菌株活化：将1% D. fangzhongdai Onc5加入20 mL的胰蛋白胨大豆液体（tryptose soya broth, TSB）培养基中，于30 ℃，150 r/min的条件下培养12 h。
1.1.2　主要试剂
细菌基因组DNA提取试剂盒、细菌总RNA快速抽提试剂盒（bacteria total RNA isolation kit）、cDNA合成试剂盒（Mightyscript First Strand cDNA Synthesis Master Mix）、2×SanTaq PCR Master Mix (with Blue Dye)、SanPrep柱式DNA胶回收试剂盒、X-Gal溶液、异丙基硫代半乳糖苷（IPTG）溶液均购自生工生物工程（上海）股份有限公司。TransStart® Top Green qPCR SuperMix（+Dye I）购自北京全式金生物技术有限公司。胰酪大豆胨琼脂培养基（tryptose soya agar, TSA）、TSB培养基与LB培养基（luria-bertani medium）由本实验室自配。
1.2　方法
1.2.1　引物设计与合成
在NCBI数据库中查找D. fangzhongdai Onc5菌株全基因组序列（PRJNA750274），获取目的基因vfmE开放阅读框ORF序列。使用Primer 5.0软件设计引物，本研究所用引物序列见表1，均由生工生物工程（上海）股份有限公司合成。
1.2.2　RT-PCR扩增目的基因序列
利用细菌基因组DNA提取试剂盒提取D. fangzhongdai Onc5菌株DNA，以此为模板进行vfmE基因扩增。PCR扩增体系：PCR Mix 12.5 μL，上、下游引物各20 pmol，DNA模板5 ng，ddH2O补足至25 μL。反应条件：94 ℃预变性5 min；94 ℃变性30 s，退火54 ℃ 45 s，72 ℃ 40 s，35个循环；72 ℃延伸10 min。凝胶电泳检测，回收产物与pUCm-T在16 ℃过夜连接，将其转化至大肠杆菌DH5α中，涂布于含氨苄霉素（ampicillin, Amp）的LB培养基，采用Amp抗性筛选与α-互补现象筛选阳性克隆转化子，送生工生物工程（上海）股份有限公司进行测序。
1.2.3　生物信息学分析
通过EXPASY在线工具ProtParam（https://web.expasy.org/protparam/）预测和分析目的基因的分子质量、理论等电点、氨基酸等理化性质；利用ProtScale（https://web.expasy.org/protscale/）在线工具分析蛋白质的亲/疏水性；通过Conserved Domain Search软件预测vfmE蛋白保守结构域；使用NCBI在线软件（https://blast.ncbi.nlm.nih.gov/Blast.cgi）比对功能和DNAMAN软件[11]对vfmE蛋白的氨基酸序列进行同源性分析；通过SignaIP-5.0（https://www.novopro.cn/tools/signalp）在线工具进行信号肽预测；利用TMHMM-2.0（https://services.healthtech.dtu.dk/services/TMHMM-2.0/）在线工具进行跨膜结构预测[12]；利用PSORTb version 3.0.3（https://www.psort.org/psortb/）在线工具进行蛋白亚细胞定位；利用SOPMA（https://npsa.lyon.inserm.fr/cgibin/npsa_automat.pl?page=/NPSA/npsa_sopma.html）在线工具对蛋白二级结构进行分析[13]；利用SWISS-MODEL（https://swissmodel.expasy.org/interactive）在线工具进行蛋白质三级结构预测[14]；利用蛋白质互作网络数据库（https://stringdb.org/）进行vfmE基因编码蛋白的互作预测[15]。
1.2.4　RT-qPCR分析
以recA为内参基因，以E-F和E-R为引物（表1），检测vfmE在D. fangzhongdai Onc5菌株侵染文心兰叶片过程中的相对表达量。取样方法参考苏初连等[16]的方法作适当调整，具体如下：选取健康文心兰的叶片与长势一致的假鳞茎，将清洗干净的叶片和假鳞茎浸泡于1% NaCIO溶液中15 min，随后用无菌水清洗3遍，置于无菌培养皿中。用无菌穿刺注射接种生长期文心兰叶片和假鳞茎，每个接种点5 µL D. fangzhongdai Onc5菌液（浓度为1×107个/mL）。选择0 h以及发病期时间点取样（3、6、9、12、18、24 h），剪取接种点周边1 cm×1 cm的叶片（包括接种点在内），每个时间点选取12个接种点，每4个接种点为一个样本，共计3个样本，液氮速冻后置于-80 ℃保存备用。
利用细菌总RNA抽提试剂盒提取D. fangzhongdai Onc5菌株总RNA，参照cDNA合成试剂盒自带试剂说明书的使用方法，对cDNA的第一链进行生物合成。实时荧光定量PCR反应体系为20 μL：TransStart® Top Green qPCR SuperMix (+Dye I) 10 μL、cDNA 1 μL、F-Primer 0.4 μL、R-Primer 0.4 μL和Nuclease-free water 8.2 μL。反应条件为：94 ℃ 30 s；94 ℃ 5 s，60 ℃ 15 s，72 ℃ 10 s，42个循环；在72 ℃时收集荧光信号。采用2-ΔΔCt法计算目的基因的相对表达量。
1.3　数据处理
采用SPSS 19.0软件处理试验数据，采用Duncan法进行样本间差异显著性分析，P<0.01表示差异显著。每组实验均重复3次。使用Origin Pro 8软件制图表。
2　结果与分析
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2.1　 vfmE基因的克隆与序列分析
如图2所示，在预期位置处出现单一条带，且条带清晰明亮。将该产物连接到pUCm-T载体上克隆测序，经序列比对分析，成功克隆D. fangzhongdai Onc5 vfmE基因。对vfmE基因序列分析后发现，该序列长564 bp，共编码187个氨基酸。通过Conserved Domain Search对该基因的氨基酸序列进行分析，显示其具有1个保守结构域，该结构域位于氨基酸序列的172~426位置，为AraC-superfamily结构域（图3），结果表明vfmE基因属于AraC转录激活蛋白家族成员。
与GenBank中注册的Dickeya属病原菌vfmE基因序列进行比对，结果表明，D. fangzhongdai Onc5 vfmE与D. dadantii 3937、D. dianthicola 16JP03、D. poaceiphila NCPPB 569、D. solani CFBP5647、D. zeae EC2、D. chrysanthemi Ech1591和D. fangzhongdai DSM 101947菌株的同源性分别为95.74%、94.86%、91.13%、96.93%、86.88%、89.18%和98.82%。
2.2　vfmE蛋白理化性质分析
蛋白质的理化性质是蛋白质研究的基础。用ExPASY的在线软件ProtParam预测蛋白质分子式为：C976H1528N278O280S9，蛋白质分子量为21.93 kDa，理论等电点（pI）为9.01，属于碱性蛋白质（>7）；不稳定指数为59.65，属于不稳定蛋白（>40）。脂溶性指数为91.28，亲水性平均系数为-0.397。氨基酸疏水性是氨基酸的一种基本性质，疏水性氨基酸位于蛋白质内部，由于其疏水性的相互作用，故在保持蛋白质三级结构上起作用。vfmE蛋白的氨基酸最大疏水位置为第47位异亮氨酸，最大值为2.044，第150位谷氨酸出现最小值-3.511（图4），推测vfmE蛋白为结构不稳定的亲水性蛋白。
2.3　信号肽、跨膜区预测及亚细胞定位
TMMHM预测结果表明，vfmE蛋白不存在跨膜结构域，不是跨膜蛋白（图5A）。SignaIP-5.0预测结果显示，vfmE蛋白不存在信号肽，不是分泌蛋白（图5B）。D. fangzhongdai Onc5 vfmE蛋白亚细胞定位预测结果表明，vfmE蛋白主要分布于细胞质，周质中也有少量分布。
2.4　vfmE蛋白高级结构预测与蛋白质互作网络分析
二级结构预测结果显示，vfmE蛋白含有3种二级结构，其中α-螺旋区域有109个氨基酸，占58.29%，延伸链区域有2个氨基酸，占1.07%，无规则卷曲有76个氨基酸，占40.64%。从蛋白质整体结构来看，α-螺旋和无规则卷曲是vfmE蛋白的主要结构元件，分散于整条多肽链（图6A）。本研究也对D. fangzhongdai Onc5 vfmE蛋白三级结构进行预测（图6B），三级结构以C6CFY9.1.A（D. zeae Ech1591菌株中AraC家族转录因子）为模版进行同源建模，同源建模中要求序列相似度大于30%[14]，本研究中序列相似度为96.26%，说明结果可靠。得到的三级结构模型由α-螺旋和无规则卷曲组成，与二级结构预测结果相同。为了揭示vfmE基因编码蛋白之间的关系，采用蛋白质互作网络数据库（PPIs）进行预测分析（图6C）。结果显示有10个蛋白质与vfmE蛋白互作，即AraC家族转录调控蛋白（ADM96899.1）、L-鼠李糖操纵子转录激活蛋白（ADM99315.1）、L-鼠李糖结合蛋白（rhaR和rhaS）、2个含AraC结构域的Rob蛋白（Right origin-binding protein）、2个转录调控蛋白（ADN00015.1和ADN00336.1）、与诱导剂l-阿拉伯糖互作的蛋白（araC）和DNA结合转录调控因子（yqhC）。
2.5　 vfmE基因在D. fangzhongdai Onc5中的表达分析
vfmE在整个侵染过程中均持续高效表达，在接种的各个时间点的表达量均高于对照组。由图7可知，vfmE在D. fangzhongdai Onc5侵染文心兰叶片和假鳞茎的过程中，其表达情况基本一致。在接种3 h后表达量明显上调；12 h表达量达到最高；接种18 h时后，表达量明显下调且趋于稳定。可见，vfmE基因在侵染的不同阶段均发挥着重要的作用。
3　讨论
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现有研究表明vfmE基因与Dickeya属病原菌的新型群体感应系统的调控有关[8,10]，但是关于vfmE基因分子特征的研究未见报道。本研究从文心兰D. fangzhongdai Onc5中克隆出vfmE基因，利用生物信息学软件对其理化性质、功能等情况进行预测分析。结果表明，文心兰vfmE基因全长564 bp，共编码187个氨基酸，且在氨基酸水平上与Dickeya属其他病原菌的同源性较高，均在86%以上，说明vfmE基因在Dickeya属病原菌中高度保守。在亲疏水性上，vfmE蛋白是一种亲水性蛋白，且该蛋白不具有信号肽序列，为不稳定蛋白；在结构上，vfmE蛋白不具备跨膜区域的结构，不属于跨膜蛋白，主要定位在细胞质，说明vfmE蛋白主要在胞内发挥作用。
vfmE蛋白具有1个保守结构域，该结构域位于氨基酸序列的172~426位置，属于AraC（amino acid response and amino sugar catabolism）超家族成员。AraC蛋白超家族广泛存在于细菌中，参与碳代谢、应激反应，到细菌毒力和致病性的多种生命活动的的调节[17-18]。汪瑶等[19]研究发现，嗜水气单胞菌（Aeromonas hydrophila）J-35株AraC家族成员aetY基因敲除后，细菌生物被膜形成能力和对斑马鱼的致病力均下降。ZHANG等[20]将AraC家族成员orf02889基因敲除后，嗜水气单胞菌LP-2菌株表型改变，主要表现为生物膜形成能力和铁载体产量上升，但对斑马鱼的致病力减弱。SAHEBI等[21]研究表明Erwinia amylovora EaUMG3菌株中yqhC基因（AraC家族成员）能够影响毒力因子的产生，如铁载体和胞外多糖amylovoran的产生，且E. amylovora EaUMG3突变体Δ yqhC的运动性及对梨的致病性均降低。以上研究表明，AraC家族成员可能直接调控某些病原菌与毒力因子、生物被膜形成、运动性相关的基因的表达。本研究通过RT-qPCR技术检测了D. fangzhongdai Onc5在侵染文心兰过程中vfmE基因的差异表达。结果显示，vfmE基因在侵染文心兰叶片和假鳞茎的各个阶段均有表达，其中在12 h的表达量最高，说明vfmE基因在侵染的不同阶段均发挥着重要的作用，参与了对D. fangzhongdai Onc5的致病调控。
本研究克隆了D. fangzhongdai Onc5中新型群体感应系统vfm中的关键调控基因vfmE，并进行生物信息学分析及其在侵染文心兰叶片过程中的差异表达进行检测，有助于进一步揭示vfmE基因的功能及其对Dickeya属病原菌致病性的调控机制。
基金
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  • 山西省科技厅基础研究计划项目(20210302124516; 20210302124502)
  • 山西省高校科技创新计划项目(2021L462)
文献
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参考文献 引证文献
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2025年第46卷第3期
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doi: 10.3969/j.issn.1000-2561.2025.03.004
  • 接收时间：2024-10-21
  • 首发时间：2026-06-25
  • 出版时间：2025-03-25
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  • 收稿日期：2024-10-21
  • 录用日期：2024-11-07
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山西省科技厅基础研究计划项目(20210302124516; 20210302124502)
山西省高校科技创新计划项目(2021L462)
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    忻州师范学院生物系，山西忻州　034000

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* 卢秋巍（LU Qiuwei），E-mail：。
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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
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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