氨基酸影响尖孢镰孢菌古巴专化型厚垣孢子的形成

丁兆建,漆艳香,曾凡云,朱为菊,许天委,彭军,谢艺贤,张欣

菌物学报 ›› 2021, Vol. 40 ›› Issue (6) : 1413-1426.

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菌物学报 ›› 2021, Vol. 40 ›› Issue (6) : 1413-1426. DOI: 10.13346/j.mycosystema.200317 CSTR: 32115.14.j.mycosystema.200317
研究论文

氨基酸影响尖孢镰孢菌古巴专化型厚垣孢子的形成

作者信息 +

Amino acid involved in chlamydospore formation of Fusarium oxysporum f. sp. cubense

Author information +
文章历史 +

摘要

香蕉枯萎病是由尖孢镰孢菌古巴专化型Fusarium oxysporum f. sp. cubense(Foc)侵染引起的一种土传真菌病害,已严重威胁香蕉产业的健康发展。该病菌产生的厚垣孢子可在土壤中存活多年,是香蕉枯萎病的初侵染源。本研究通过氨基酸添加试验,证明添加甘氨酸可抑制厚垣孢子的形成;通过对该病菌厚垣孢子形成前期、初期、中期和后期的转录组分析,发现氨基酸合成通路中有93个基因的表达水平在厚垣孢子形成过程中发生了显著变化;In silico 分析表明其中10个基因参与调控真菌的氨基酸合成,11个基因参与调控真菌种的生长发育和产孢,19个基因参与调控真菌种的致病性和毒素产生。由此推测,氨基酸合成通路不仅与尖孢镰孢菌古巴专化型厚垣孢子的形成相关,其有可能参与调控该病菌的致病性。

Abstract

Fusarium wilt of banana is a devastative soil-borne fungal disease, caused by Fusarium oxysporum f. sp. cubense (Foc) and it is a serious threat to health production of banana. Chlamydospores abundantly produced by Foc could survive for many years in the infected-soil as primary infection sources of the disease. The experimental results indicate that chlamydospore formation of Foc is evidently inhibited by supplement of glycine in the induction system. Transcriptome analyses of mycelial growth, and chlamydospore formation in initial and afterwards developing stages revealed that expression levels of 93 genes varyied in amino acid biosynthesis pathway. Among them, 10 genes were involved in the regulation of fungal amino acid biosynthesis, 11 genes involved in the regulation of fungal growth and conidial formation, and the other 19 genes in the regulation of fungal virulence and toxin production. These results confirm that glycine is involved in chlamydospore formation and virulence of Foc.

关键词

香蕉枯萎病 / 甘氨酸 / 形态发育 / 差异表达基因

Key words

Fusarium wilt of banana / glycine / morphological development / differential expression genes

引用本文

导出引用
丁兆建, 漆艳香, 曾凡云, 朱为菊, 许天委, 彭军, 谢艺贤, 张欣. 氨基酸影响尖孢镰孢菌古巴专化型厚垣孢子的形成[J]. 菌物学报, 2021, 40(6): 1413-1426 https://doi.org/10.13346/j.mycosystema.200317
DING Zhao-Jian, QI Yan-Xiang, ZENG Fan-Yun, ZHU Wei-Ju, XU Tian-Wei, PENG Jun, XIE Yi-Xian, ZHANG Xin. Amino acid involved in chlamydospore formation of Fusarium oxysporum f. sp. cubense[J]. Mycosystema, 2021, 40(6): 1413-1426 https://doi.org/10.13346/j.mycosystema.200317
冬虫夏草是冬虫夏草菌Ophiocordyceps sinensis寄生于蝙蝠蛾Hepialus armoricanus幼虫体后发育成的真菌子座和充满菌丝的僵死幼虫的复合体(Zhou et al. 2014;Liu et al. 2015;Lu et al. 2016),是我国传统的名贵中草药。冬虫夏草菌是学术界普遍认同的冬虫夏草无性型(刘锡琎等 1989;李增智等 2000;Chen et al. 2001;莫明和等 2001;刘作易等 2003;谢放等 2011)。随着组学技术的快速发展,挖掘冬虫夏草有性启动、宿主侵染、代谢物合成等的关键基因,成为了目前该领域的研究热点。
实时荧光定量PCR(qRT-PCR)现已成为不同样品之间进行基因表达水平定量差异比较的权威性方法(Nolan et al. 2006)。在实时荧光定量PCR试验中,为了消除由于材料、反应效率等因素导致基因表达数据的误差,通常将持家基因作为研究的内参基因对数据进行标准化处理,以此来减小研究误差(Foldager et al. 2009),这就要求所选择的内参基因在所有的研究材料中都必须稳定表达。然而,越来越多的研究表明,在某种试验稳定表达的内参基因,在另一种试验中有可能是变化的(Jain et al. 2006;Løvdal & Lillo 2009;Tong et al. 2009)。而在任何试验条件下都能稳定表达的内参基因几乎不存在(Li et al. 2016;Rui et al. 2016)。因此要针对于不同的试验条件选择最适合的内参基因,以此来提高试验数据的准确性。目前,内参基因的筛选在灵芝Ganoderma lingzhiXu et al. 2014)、毛木耳Auricularia corneaJia et al. 2019)、黑木耳Auricularia heimuer张越等 2020)、香菇Lentinula edodesXiang et al. 2018)、糙皮侧耳Pleurotus ostreatusFernández-Fueyo et al. 2014)、刺芹侧耳Pleurotus eryngii秦晓艺和王杰 2015)等重要的食药用菌中已有报道,而冬虫夏草研究领域未见相关报道。
在以往研究中,绝大多数都是用组织分离方法从野生冬虫夏草中获取冬虫夏草菌丝体作为研究材料。在冬虫夏草菌培养过程中,会出现3种有明显差异的菌丝形态(图1),但其发生的原因和机理未见报道。为排除可能是混入的杂菌干扰,我们通过单子囊孢子纯化菌株对这一现象开展研究,排除了杂菌因素,发现在形态、弯曲程度、致密程度、显微表面结构及产孢能力等方面均存在显著差异。因此,以冬虫夏草菌3种菌丝形态为研究材料来筛选冬虫夏草菌菌丝体时期表达最为稳定的内参基因,能为冬虫夏草组学研究提供重要的参考依据。
图1 三种菌丝形态图

A:气生菌丝;B:菌丝团;C:基生菌丝

Fig. 1 Morphology of hyphae.

A: Aerial mycelium; B: Hyphal knot; C: Substrate mycelium.

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本研究以冬虫夏草菌单孢菌株的3种菌丝形态为材料,选择了11个持家基因,利用geNorm、NormFinder、BestKeeper 3种分析程序进行了分析评价,并用RefFinder程序进行了综合排比,筛选出了冬虫夏草菌菌丝体时期表达最为稳定的内参基因。

1 材料与方法

1.1 供试菌株的准备

使用本课题组利用单个子囊孢子培养得到的单孢菌株为供试菌株,编号为TZ8-1,现保存于兰州交通大学生物种苗工程研究所。分别取气生菌丝(A)、菌丝团(B)和基生菌丝(C)3种菌丝形态(图1)为试验材料,每组取3个生物学重复样本,-80℃冰箱保存,用于内参基因的筛选研究。

1.2 候选内参基因的选择与引物设计

选择11个常见的持家基因为内参候选基因,分别是18S核糖体RNA(18S rRNA)、腺嘌呤磷酸核糖转移酶(APRTase)、β-微管蛋白(β-TUB)、核糖体蛋白L2(RPL2)、翻译延长因子1-a(EF1-α)、磷酸葡萄糖异构酶(PGI)、磷酸葡萄糖变异酶(PGM)、质膜质子ATP酶(H+-ATPase)、肌动蛋白1(ACT1)、多聚泛素酶(UBQ)和3-磷酸甘油脱氢酶(GAPDH)。引物序列根据NCBI中Ophiocordyceps sinensis CO18(ASM44836v1)的基因组序列信息,经由上海欧易生物医学科技有限公司设计并由北京擎科新业生物技术有限公司合成,引物序列见表1
表1 候选内参基因的引物序列

Table 1 Primer sequences of candidate internal reference genes

基因名称
Gene name
正向引物
Forward primer (5’-3’)
反向引物
Reverse primer (5’-3’)
扩增产物
Amplicon size (bp)
Tm
(°C)
18S rRNA GCAGTGGCATCTCTCAGTC TCATCGATGCCAGAACC 128 60
APRTase ATGCTGAGCTGTTTAGCG TGCCCTGTTCGTCGTAGA 90 60
β-TUB TACGCCTCTTCGACGATAG GCCGTTGTAGACACCATT 148 60
RPL2 ACCTACCGTCTCCATCAT GTGAACCTGCTGGACAAT 109 60
EF1-α CAAGGGCTCTTTCAAGTATGC GTGACATAGTACCTGGGAGT 114 60
PGI TTCGACCAGTATCTTCATCGC GTGTACTTGACCGACGATCC 83 60
PGM AAGCCCTTTCAGGACCAA GAACGACTCGGTGTAGTG 87 60
H+-ATPase CGCTTCGCGGAAATCTATAC AGACGTTCTTGTTGACGG 90 60
ACT1 CAATCGGCACAACTGGACA GACGACCTGAGCGGAATA 95 60
UBQ CGACATCGAGTTGGACTAC ATACCTGCAATCTGTCCG 82 60
GAPDH GAGGCCGAGAGCCAACTA TTCATCACGACAGCACCA 99 60

1.3 样品总RNA的提取及cDNA的合成

采用试剂盒(mirVana™ miRNA ISOlation Kit,Ambion-1561)提取总RNA,之后利用NanoDrop 2000分光光度计(Thermo Scientific,USA)测定浓度及OD260/OD280,琼脂糖凝胶电泳检测RNA完整性。检测合格后利用TransScript All-in-One First-Strand cDNA Synthesis SuperMIX for qPCR试剂盒将待测RNA逆转录成cDNA。反转录体系为:总RNA 0.5μg;5×TransScript All-in-one SuperMix for qPCR 5μL;gDNA Remover 0.5μL;Nuclease- free H2O加至10μL。反应程序:42℃ 15min,85℃ 5s。逆转录完毕后加入90μL Nuclease- free H2O储存在-20℃冰箱备用。

1.4 荧光定量PCR

利用PerfectStartTM Green qPCR SuperMix试剂盒在LightCycler® 480 Ⅱ型荧光定量PCR仪(Roche,Swiss)上进行反应。反应体系:2×PerfectStartTM Green qPCR SuperMix 5μL;10μmol/L Forward primer 0.2μL;10μmol/L Reverse primer 0.2μL;cDNA 1μL;Nuclease- free H2O 3.6μL。PCR程序:94℃ 30s;94℃ 5s;60℃ 30s;45个循环。循环结束后利用熔解曲线检测产物特异性:从60℃缓慢升温至97℃,每℃采集5次荧光信号。

1.5 表达稳定性分析

qRT-PCR扩增完毕后,利用geNorm(Vandesompele et al. 2002)、NormFinder(Andersen et al. 2004)和BestKeeper(Pfaffl et al. 2004)3种软件分析11个候选内参基因的表达差异。利用RefFinder(Zsori et al. 2013)软件对11个候选内参基因的表达稳定性进行综合排名。

2 结果与分析

2.1 RNA的分离与纯化

RIN(RNA integrity number),代表RNA完整性数值,范围在1-10之间,是Agilent Bioanalyzer对total RNA完整性给出的数字化评估,数值越小说明降解越严重。RIN值在1-6之间说明RNA发生明显降解,RIN值在7-10之间说明RNA完整性较好。18S与28S是真核生物rRNA的两个主要亚基,如果28S/18S为1.8-2.0表明所提取RNA完整性较好,基本无降解发生,当28S/18S小于0.7时,表明已经发生较明显的降解,该样品不可用于后续分析(易乐飞等 2016;Padhi et al. 2018)。本研究中RNA样品的质检结果见表2,RIN值均在7以上,28S/18S值均在0.7以上,说明所有样品符合后续分析要求。
表2 RNA质检结果

Table 2 Results of RNA quality control

样本
Sample
浓度
Concentration (μg/μL)
A260/280 A260/230 体积
Volume (μL)
总量
Total (μg)
28S/18S RIN
A1 0.3864 2.18 1.84 20 7.73 1.7 9.5
A2 0.1979 2.19 2.28 20 3.96 0.9 7.7
A3 0.1701 2.14 1.78 20 3.40 1.0 7.2
B1 0.3490 2.18 1.81 20 6.98 1.7 10.0
B2 0.2323 2.17 1.77 20 4.65 2.1 9.2
B3 0.1352 2.16 1.75 15 2.03 1.2 7.1
C1 0.3873 2.16 2.24 20 7.75 1.5 8.8
C2 0.5354 2.23 2.00 20 10.71 1.1 7.9
C3 0.2250 2.16 2.10 20 4.50 1.3 7.9

2.2 候选内参基因的引物分析

12个候选内参基因引物进行qRT-PCR扩增得到的熔解曲线均为单一熔解峰(图2),这说明所设计的引物具有较强的特异性,定量分析结果可靠性高。
图2 由qRT-PCR产生的熔解曲线

横坐标:温度;纵坐标:-(d/dt) Fluorescence (465-510)

Fig. 2 Melting curve generated by qRT-PCR.

Abscissa: Temperature; Ordinate: -(d/dt) fluorescence (465-510).

Full size|PPT slide

2.3 候选内参基因的Ct值分析

11个候选内参基因在不同形态菌丝样本中Ct值的分布箱形图见图3,Ct值的变化范围可以体现其转录水平在不同样品中的离散程度。11个候选内参基因的Ct值均在9-31之间,其中RPL2的Ct值变化范围最大,相差3.07个循环,APRTase的Ct值变化范围最小,相差1.13个循环。可以看出,11个不同的候选内参基因在不同菌丝形态的样本中转录水平存在不同程度的差异。因此,在不同样本中筛选出表达最为稳定的内参基因极为重要。
图3 Ct值分布箱形图

Fig. 3 Distribution of Ct values.

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2.4 候选内参基因的表达稳定性分析

2.4.1 geNorm分析结果:geNorm是专门用于Real-time PCR中筛选内参基因及确定最适内参基因数目的程序,可用于筛选任何实验的任意数目的内参基因,并最终挑选出两个或两个以上的内参基因组合来校正数据,可使相对定量的结果更为精确(吴建阳等 2017)。该程序通过计算出每个候选内参基因稳定性的M值来筛选出稳定性较好的内参基因,判定标准为M值小于1.5即可作为内参基因,M值越小内参基因的稳定性越好(Vandesompele et al. 2002)。
11个候选内参基因通过geNorm程序分析发现,M值均小于1.5,因此,11个候选内参基因均可作为冬虫夏草菌菌丝体时期不同形态的内参基因。其中,候选内参基因UBQ与PGM的M值最小。结果显示11个候选内参基因的稳定性依次为PGM、UBQ>EF-1α> RPL2>β-TUB>PGI>18S rRNA>ACT1>H+-ATPase> APRTase>GAPDH(图4)。
图4 十一个候选内参基因的稳定性折线图

Fig. 4 Broken line diagram of the stability of 11 candidate reference genes.

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2.4.2 NormFinder分析结果:NormFinder程序计算原理与geNorm程序相似,也是先获得内参基因表达稳定值,再根据稳定值大小来筛选出最合适的内参基因,判定标准为表达稳定值最小的内参基因为最合适的内参基因(Andersen et al. 2004;吴建阳等 2017)。
NormFinder程序对冬虫夏草菌的11个候选内参基因表达稳定性的分析结果见表3,稳定值越低,基因表达越稳定,因此所得到最为稳定内参基因为UBQ。
表3 NormFinder分析候选内参基因的表达稳定值

Table 3 NormFinder analysis of the stable expression values of the candidate reference genes

基因名称
Gene name
稳定值
Stability value
最优基因
Best gene
UBQ 0.096 UBQ
PGM 0.102
ACT1 0.122
H+-ATPase 0.140
EF-1α 0.155
18S rRNA 0.223
APRTase 0.269
PGI 0.292
β-TUB 0.350
RPL2 0.363
GAPDH 0.646
2.4.3 BestKeeper分析结果:BestKeeper程序是针对内参基因和目标基因表达量分析的程序,最多只能比较100个样品中10个内参基因和10个目标基因的表达水平。通过该程序可计算获得每个基因之间产生配对的相关系数(r)、标准偏差(SD)和变异系数(CV),在通过比较各个值的大小,最终确定稳定性较好的内参基因,判定原则为相关系数越大,标准偏差和变异系数越小,内参基因的稳定性越好,反之稳定性越差。当SD>1时,则该内参基因表达不稳定(Pfaffl et al. 2004;吴建阳等 2017)。BestKeeper程序分析11个候选内参基因的稳定性结果见表4,11个候选内参基因的SD均小于1,这进一步说明11个候选内参基因均可作为冬虫夏草菌菌丝体时期的内参基因。根据每个内参基因Ct值的标准差(SD)和变异系数(CV)综合排名前三的内参基因分别是APRTase、ACT1和H+-ATPase。
表4 BestKeeper程序分析候选内参基因的稳定性表达

Table 4 BestKeeper program analyzes the stability expression of candidate reference genes

基因名称
Gene name
变异系数
CV
标准差
SD
APRTase 1.23 0.33
ACT1 1.68 0.43
H+-ATPase 1.8 0.53
UBQ 2.17 0.65
PGM 2.97 0.69
18S rRNA 4.31 0.7
GAPDH 2.37 0.7
EF-1A 3.9 0.73
PGI 3.65 0.86
β-TUB 3.9 0.88
RPL2 3.86 0.9

2.5 内参基因组合数分析

2.5.1 RefFinder综合分析结果:RefFinder是一个很好的网络综合分析工具,可用于实验数据评估和内参基因的筛选。集成了目前内参基因筛选可用的主要计算程序(geNorm、Normfinder、BestKeeper等),对候选内参基因进行比较和排序。会根据每个程序的排名,给每个候选内参基因赋予一个适当的权重,并计算出其权重的几何平均值,从而得出最终的总排名(Xie et al. 2012;Zsori et al. 2013)。
通过RefFinder对几种分析程序分析结果进行综合排名,11个候选内参基因综合排比结果前三的分别是UBQ、PGE和ACT1,后三名分别是GAPDH、RPL2和β-TUB(表5)。
表5 RefFinder综合排名结果

Table 5 Comprehensive ranking results of RefFinder

基因名称
Gene name
Delta CT排名
Delta CT ranking
geNorm排名
geNorm ranking
NormFinder排名
NormFinder ranking
BestKeeper排名
BestKeeper ranking
几何均值
Geomean
综合排名
Comprehensive
ranking
UBQ 2 2 1 4 1.78 1
PGM 1 1 2 5 1.86 2
ACT1 4 8 3 2 4.12 3
EF-1α 3 3 5 8 4.49 4
H+-ATPase 5 9 4 3 5.18 5
APRTase 8 10 7 1 5.79 6
18S rRNA 6 7 6 6 6.48 7
PGI 7 6 8 9 7.16 8
β-TUB 9 5 9 10 8.17 9
RPL2 10 4 10 11 8.32 10
GAPDH 11 11 11 7 10.84 11
2.5.2 两两变异分析:geNorm软件通过两两比较(Vn/n+1)可以确定最佳内参基因的数量。在此过程中默认的V值为0.15,当Vn/n+1值小于0.15时,无需引入额外的内参基因(吴建阳等 2017)。如果内参基因的平均M值小于0.2,则认为该基因是稳定的(Jia et al. 2019)。在本研究中最低M值小于0.2,并且V值均在0.15以下(图5),这说明有一个内参基因就可以对基因表达数据进行归一化处理,而为了结果更加可靠,引入两个内参基因的效果会更好。因此,根据M值的大小,判断出UBQ和PGM这两者是最好的组合。
图5 十二个候选内参基因两两变异(Vn/n+1)分析

Fig. 5 Pairwise variation analysis of 12 candidate reference genes (Vn/n+1).

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3 讨论

大量研究表明,不同试验条件下内参基因的选择有所不同,不存在不同物种或不同试验条件下通用的内参基因(Xu et al. 2014;赵小龙 2016;Xiang et al. 2018;张倩倩等 2018;Jia et al. 2019)。本研究采用最适生长条件下生长120d后的冬虫夏草菌单孢菌株的3种菌丝形态为试验材料,筛选了冬虫夏草菌菌丝体时期最适的内参基因,所得到的结果仅限于为类似试验体系提供参考,并不能保证所有试验体系适用,尤其以子实体为研究材料的相关实验体系可能还需要进一步验证。
在候选内参基因上,本研究选择了11个典型的持家基因作为候选内参基因,在选取数量上多于其他食药用真菌的相关研究(Xu et al. 2014;安丹丹等 2016;赵小龙 2016;Xiang et al. 2018;Jia et al. 2019),因此本研究所得结果可靠性更好。但由于机体中持家基因数目庞大,因此本研究选取的也只不过是冰山一角。本研究所获得的结果良好,所选取的11个候选内参基因通过geNorm分析所得的M值范围在0.15-0.58之间,且Vn/n+1值均小于0.15,这说明本研究所选取的11个候选内参基因均可作为冬虫夏草菌菌丝体时期的内参基因,完全能为该领域研究提供参考,而无需再做过多验证。
本研究在候选基因稳定性分析过程中发现,选择不同的分析程序所得到的结果有所差异,如APRTase在BestKeeper分析结果中稳定性最好,但在geNorm和NormFinder分析结果中却处于末端。这种现象在其他物种内参基因筛选中也同样出现(Xu et al. 2014;Tao et al. 2016;Qian et al. 2018;Xiang et al. 2018),究其原因是BestKeeper程序分析统计的算法和侧重点有别于geNorm和NormFinder分析程序。而本研究通过引入RefFinder对各程序所得结果进行综合排名,很好地解决这了一问题,因此,参考RefFinder程序的综合排名结果,可靠性会更好。

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基金

国家自然科学基金(31801690)
2019 年海南省基础与应用基础研究计划高层次人才项目(2019RC249)
现代农业产业技术体系专项(CARS-31-07)
琼台师范学院校级项目(qtyb201910)

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