Expression patterns of lncRNA5334 and its cis-acting genes in Nosema ceranae
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摘要:目的
本研究旨在揭示东方蜜蜂微孢子虫Nosema ceranae侵染意大利蜜蜂Apis mellifera ligustica工蜂过程中lncRNA5334的表达模式和调控作用,为进一步探究lncRNA5334的作用机制提供基础。
方法通过RT-PCR验证东方蜜蜂微孢子虫lncRNA5334的表达。利用相关软件预测lncRNA5334顺式调控的靶基因,并采用RT-qPCR检测lncRNA5334及其靶基因在侵染过程中的相对表达量。
结果在接种东方蜜蜂微孢子虫的意大利蜜蜂工蜂1dpi(1 day post inoculation)、2 dpi,3dpi和4 dpi的中肠样品及东方蜜蜂微孢子虫孢子样品中均扩增出符合预期大小(约185 bp)的目的片段,而在未接种孢子的工蜂中肠中未检测到目的片段;相较于1 dpi,lncRNA5334的表达量在2 dpi下调(P > 0.05),在3 dpi和4 dpi均显著下调(P < 0.05),总体呈持续下降的表达趋势;lncRNA5334潜在调控4个上下游基因(Pol Ⅱ,Trx,ACS和GPDH)的转录;Pol Ⅱ的表达量在2 dpi和3 dpi上调(P > 0.05),在4 dpi显著上调(P < 0.05);Trx的表达量在2 dpi,3 dpi和4 dpi皆显著上调(P < 0.05);ACS的表达量在2 dpi和4 dpi均上调(P > 0.05),在3 dpi显著上调(P < 0.05);GPDH的表达量在2 dpi下调(P > 0.05),在3 dpi和4 dpi均显著上调(P < 0.05)。
结论研究结果表明lncRNA5334在东方蜜蜂微孢子虫孢子及侵染过程中均表达,lncRNA5334可能通过顺式作用调控Pol Ⅱ,Trx,ACS和GPDH的转录进而调节东方蜜蜂微孢子虫侵染意大利蜜蜂工蜂的过程。
Abstract:AimThe aim of this study is to reveal the expression pattern and regulatory role of lncRNA5334 during the process of Nosema ceranae infection of Apis mellifera ligustica workers, providing a basis for further investigation of the regulatory mechanism of lncRNA5334.
MethodsThe expression of lncRNA5334 in Nosema ceranae was verified by RT-PCR. Relevant software were utilized to predict the target genes regulated by lncRNA5334 in cis-acting manner. RT-qPCR was used to detect the relative expression of lncRNA5334 and its target genes during the infestation process.
ResultsThe results showed that the target fragment of the expected size (approximately 185 bp) was amplified from the N. ceranae spore sample and from the midgut samples of Apis mellifera ligustica workers at 1 dpi (1 day post inoculation), 2 dpi, 3 dpi, and 4 dpi with Nosema ceranae, while no target fragment was detected in the midgut samples of uninoculated workers; as compared with that at 1 dpi, the expression level of lncRNA5334 was downregulated at 2 dpi (P > 0.05) and significantly downregulated at 3 dpi and 4 dpi (P < 0.05), presenting an overall trend of continuous decrease in expression; lncRNA5334 potentially regulated the transcription of four up- and down-stream genes (Pol Ⅱ, Trx, ACS, and GPDH); the expression level of Pol Ⅱ was up-regulated at 2 dpi and 3 dpi (P > 0.05) and significantly up-regulated at 4 dpi (P < 0.05), the expression level of Trx was significantly up-regulated at 2 dpi, 3 dpi and 4 dpi (P < 0.05), the expression level of ACS was up-regulated at 2 dpi and 4 dpi (P > 0.05) and significantly up-regulated at 3 dpi (P < 0.05), the expression level of GPDH was down-regulated at 2 dpi (P > 0.05) while significantly up-regulated at both 3 dpi and 4 dpi (P < 0.05).
ConclusionThese results suggest that lncRNA5334 is expressed in the spore and during the infection process of Nosema ceranae, and lncRNA5334 may potentially modulate the process of Nosema ceranae infection in Apis mellifera ligustica through cis-acting manner through modulating the transcription of Pol Ⅱ, Trx, ACS, and GPDH.
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东方蜜蜂微孢子虫Nosema ceranae是一种常见的蜜蜂病原真菌,主要寄生成年蜜蜂中肠上皮细胞,对蜂王、工蜂和雄蜂均具有侵染性(梁勤和陈大福,2009)。目前,东方蜜蜂微孢子虫广泛感染世界各地的饲养蜂群和自然蜂群(Paris et al.,2018)。东方蜜蜂微孢子虫感染可对蜜蜂宿主造成一系列负面影响,包括免疫抑制、凋亡抑制、行为变化和寿命缩短等,严重危害蜂群健康与养蜂业可持续发展(陈恒等,2022)。
长链非编码RNA(Long non-coding RNA, lncRNA)指长度大于200 nt的线性RNA分子,通过与DNA, RNA或蛋白质相互作用来调节基因转录、细胞分化、疾病发生及免疫应答等诸多生命活动(Herman et al.,2022)。LncRNA具有多种调控方式,包括顺式作用(Cis-acting)、反式作用(Trans-acting)和竞争性内源RNA(Competing endogenous RNA, ceRNA)网络等。随着高通量测序技术的快速发展,智人Homo sapiens(Wu et al.,2020)、果蝇Drosophila(Talross et al.,2023)、西方蜜蜂Apis mellifera(Jayakodi et al.,2015)和拟南芥Arabidopsis thaliana(Jin et al.,2023)等的lncRNA被陆续鉴定出来。但真菌lncRNA的研究较为滞后,蜜蜂病原的相关研究更为匮乏。Guo等(2018b)利用RNA-seq和生物信息学在蜜蜂球囊菌Ascosphaera apis中鉴定到379条lncRNA,并通过比较分析发现蜜蜂球囊菌的lncRNA和mRNA具有类似的结构特征。Lin等(2020)通过高通量测序技术对狄斯瓦螨Varroa destructor的lncRNA进行了全转录组鉴定,共鉴定出6645条lncRNA,并发现相较于mRNA,上述lncRNA的转录本长度和ORF长度均更短,外显子更少,表达水平更低。
目前,东方蜜蜂微孢子虫lncRNA的研究十分有限且进展缓慢,迄今仅有两例报道。本团队前期通过转录组测序在东方蜜蜂微孢子虫孢子样品中鉴定到83条lncRNA,并通过RT-PCR验证了其中12条lncRNA的表达(Guo et al.,2018a);进一步解析了东方蜜蜂微孢子虫lncRNA的调控方式和潜在作用。在上述鉴定到的83条东方蜜蜂微孢子虫lncRNA中,包括lncRNAs、基因间区长非编码RNA(LincRNA)和正义链lncRNA(Sense lncRNA)。本研究对前期鉴定到的lncRNA5334进行表达验证,预测其顺式调控的靶基因并进行相关分析,进而检测lncRNA5334及其关键靶基因在东方蜜蜂微孢子虫侵染意大利蜜蜂Apis mellifera ligustica工蜂过程中的表达模式,以期明确lncRNA5334的调控作用及lncRNA5334和靶基因在侵染过程中的表达规律,为进一步探究其功能和机制提供科学依据。
1. 材料与方法
1.1 供试生物材料
意大利蜜蜂工蜂取自福建农林大学蜂学与生物医药学院宿主—病原互作机制及精准医学团队的实验蜂群。东方蜜蜂微孢子虫孢子由本实验室分离和纯化(刘彩珍等,2024),并保藏于中国普通微生物菌种保藏管理中心,保藏号NO. 28110。
按照本实验室已建立的技术流程(Chen et al.,2019;孙明会等,2023)进行意大利蜜蜂工蜂接种及样品制备:(1)从群势较强、外观健康且未受东方蜜蜂微孢子虫感染的意大利蜜蜂蜂群中提取封盖子脾至实验室,放入温度为(34 ± 0.5)℃,相对湿度70%的恒温恒湿箱;(2)收集刚羽化出房的工蜂,经2 h饥饿处理后,用移液器对工蜂(n=35)接种5 μL 50%(w/v)蔗糖溶液(含106个东方蜜蜂微孢子虫孢子),待蔗糖溶液食尽后将上述工蜂放入干净的塑料盒,上方插入一支装有2 mL蔗糖溶液的饲喂器;(3)每24 h更换一支饲喂器,每日检查工蜂的死亡情况,及时清理死亡工蜂;(4)分别在接种后1天(1 Day post inoculation, 1 dpi), 2 dpi, 3 dpi和4 dpi,用灭菌处理的眼科镊小心拉取工蜂中肠,每3头中肠放入1个无菌的RNA-Free离心管,液氮速冻后迅速转移至-80℃超低温冰箱保存备用。
1.2 RT-PCR验证
根据本团队前期进行转录组测序获得的lncRNA5334序列(GenBank登录号: NW_003314142.1),利用Primer Premier 6软件设计并合成lncRNA5334的特异性上下游引物(表 1)。使用RNA抽提试剂盒(Promega公司,美国)分别提取1.1节制备的1 dpi-4 dpi的工蜂中肠样品及东方蜜蜂微孢子虫孢子样品的总RNA,逆转录得到cDNA,作为模板进行PCR扩增。反应体系和条件按王紫馨等(2023)的报道设置。产物先进行1.5%琼脂糖凝胶电泳,再置于核酸凝胶成像仪(上海培清,中国)下观察和拍照。
表 1 本研究使用的引物序列Table 1 Sequences of primers used in this study名称Name 序列(5'-3') Sequence (5'-3') lncRNA5334-F GGCAGAATACTACGGCATA lncRNA5334-R ACACGGCTATTGTCCTTAG actin-F ACAATGGTTCAGGTATCGTA actin-R GTGCCTCATCTCCTACATAA Trx-F GGGATTTGGCATACTTCTA Trx-R CCCATATCATGTATTGTGTG ACS-F TGGCAGACAGAAACTGGTGGAA ACS-R GGTAAAGACGCACACTCAGGCT Pol Ⅱ-F AGAGAAAGAAACACATAGTCTTGGT Pol Ⅱ-R AGGATGGCATACTTTGTAAGAACT GPDH-F TGGTGTTACGGTTGGTCTAGGA GPDH-R GGCAATACCACACGACTGGAAT 1.3 LncRNA5334顺式调控基因预测
参照熊翠玲等(2018)的方法,搜索lncRNA上下游10 kb内的蛋白编码基因,作为lncRNA潜在顺式调控的靶基因。通过Nr数据库(https://www.ncbi.nlm.nih.gov/protein)进行靶基因的注释分析。
1.4 RT-qPCR检测
根据1.3节预测出的靶基因的Nr数据库注释,在GenBank数据库(https://www.ncbi.nlm.nih.gov/genbank/)中查询相应的核苷酸序列。利用Primer Premier 6软件设计靶基因及内参基因actin(GenBank登录号: 36320842)的特异性引物(表 1)。使用1.2节得到的cDNA作为lncRNA5334和靶基因的qPCR模板。反应在Quant Studio 3荧光定量PCR仪(ABI,美国)上进行,条件和体系参照郭意龙等(2022)的报道进行设置。每个反应均设置3个生物学重复和3次技术重复。以1 dpi作为参照,采用2-△△Ct法计算lncRNA5334及其靶基因在2 dpi, 3 dpi和4 dpi的相对表达量。通过GraphPad Prism 8软件进行数据分析和绘图,并利用SPSS Statistics 20软件进行单因素方差分析(ANOVA),以P < 0.05为显著性阈值。使用Tukey检验法和字母显著标记法两两比较分析实验数据。
2. 结果与分析
2.1 东方蜜蜂微孢子虫孢子和侵染过程中lncRNA5334的表达验证
琼脂糖凝胶电泳结果显示,在东方蜜蜂微孢子虫孢子样品中扩增出符合预期大小(约185 bp)的目的片段,在1~4 dpi的工蜂中肠样品中也扩增出长度约185 bp的目的片段,但在未接种的工蜂中肠样品中未扩增出上述目的片段(图 1)。
图 1 东方蜜蜂微孢子虫lncRNA5334扩增产物的琼脂糖凝胶电泳注:泳道M,DNA marker;泳道N,未接种东方蜜蜂微孢子虫孢子的1日龄意大利蜜蜂工蜂中肠样品(阴性对照);泳道P,东方蜜蜂微孢子虫孢子样品(阳性对照);泳道1~4,东方蜜蜂微孢子虫接种后1~4 d的工蜂中肠样品。Fig. 1 Agarose gel electrophoresis for the amplification products from lncRNA5334 in Nosema ceranaeNote: Lane M, DNA marker; lane N, The midgut sample from un-inoculated Apis mellifera ligustica 1-day-old worker (negative control); lane P, Nosema ceranae spore sample (positive control); lanes 1~4, The midgut samples from Apis mellifera ligustica worker at 1~4 days post inoculation with Nosema ceranae.2.2 LncRNA5334的顺式调控作用分析
顺式作用分析结果显示,lncRNA5334潜在调控4个上下游基因,包括硫氧还蛋白基因Trx,乙酰辅酶A合成酶基因ACS,DNA定向RNA聚合酶Ⅱ基因Pol Ⅱ,甘油-3-磷酸脱氢酶基因GPDH(表 2)。
表 2 LncRNA5334顺式调控的上下游基因概览Table 2 Overview of upstream and downstream genes regulated by lncRNA5334 in a cis-acting manner基因ID Gene ID Nr数据库注释Nr database annotation XM_024474896.1 Nosema ceranae thioredoxin family (AAJ76_270006410) XM_024476690.1 Nosema ceranae acetyl-coenzyme A synthetase (AAJ76_970005584) XM_024476687.1 Nosema ceranae DNA-directed RNA polymerase Ⅱ (AAJ76_970003904) XM_024476686.1 Nosema ceranae glycerol-3-phosphate dehydrogenase (AAJ76_970003126) 2.3 LncRNA5334在东方蜜蜂微孢子虫侵染意大利蜜蜂工蜂过程的表达模式
RT-qPCR结果显示相较于1 dpi,lncRNA5334的表达量在2 dpi下调(P > 0.05),在3 dpi和4 dpi均显著下调(P < 0.05),总体呈持续下降的表达趋势(图 2)。
图 2 东方蜜蜂微孢子虫侵染意大利蜜蜂工蜂过程中lncRNA5334的相对表达量注:图中数据为平均值±标准误;柱上不同字母表示差异显著(P < 0.05,Tukey氏检验)。下同。Fig. 2 Determination of relative expression level of lncRNA5334 during Nosema ceranae's infection of Apis mellifera ligustica workersNote: Data in the figure were mean ± SE; different letters above bars indicated significant difference (P < 0.05, Tukey's test). The same below.2.4 东方蜜蜂微孢子虫侵染意大利蜜蜂工蜂过程中4个上下游基因的表达模式
检测结果显示相较于1 dpi, Pol Ⅱ的表达量在2 dpi和3 dpi上调(P > 0.05),在4 dpi显著上调(P < 0.05)(图 3-A);GPDH的表达水平在2 dpi下调(P > 0.05),3 dpi和4 dpi显著上调(P < 0.05)(图 3-B)。
相比于1 dpi,Trx的表达水平在2 dpi,3 dpi和4 dpi均显著上调(P < 0.05)(图 4-A);ACS的表达量在2 dpi和4 dpi表达量均上调(P > 0.05),在3 dpi显著上调(P < 0.05)(图 4-B)。
3. 结论与讨论
LncRNA已被证实参与病原真菌的环境应激、营养获取和增殖等过程(Wang et al.,2019)。隐孢子虫Cryptosporidium parvum的lncRNA可被递送到宿主细胞核中,通过胁迫宿主组蛋白修饰系统来调控宿主基因,进而影响宿主的免疫防御(Li et al.,2021)。东方蜜蜂微孢子虫孢子是一种休眠态,仅维持低水平的生命活动。本团队前期研究发现,东方蜜蜂微孢子虫孢子可表达较丰富的miRNA、lncRNA和circRNA(Guo et al.,2018a;Guo et al.,2018c;张文德等,2022),说明孢子中发生较为活跃的基因转录活动。本研究中,在东方蜜蜂微孢子虫孢子和1~4 dpi的工蜂中肠中均鉴定到大小约185 bp的目的片段,说明lncRNA5334在东方蜜蜂微孢子虫的孢子及侵染过程中均有表达。这暗示lncRNA5334不仅参与调节孢子中的生命活动,而且参与调控东方蜜蜂微孢子虫的侵染过程。东方蜜蜂微孢子虫在西方蜜蜂工蜂中肠上皮细胞中的增殖周期约为4 d(Gisder et al.,2011)。本研究发现相较于1 dpi,东方蜜蜂微孢子虫lncRNA5334的表达量在2 dpi下调,在3 dpi和4 dpi均显著下调(图 2),表明东方蜜蜂微孢子虫侵染工蜂的过程中伴随着lncRNA5334表达水平的持续下降。推测lncRNA5334在东方蜜蜂微孢子虫的侵染过程中发挥重要的调控作用。
LncRNA的调控方式较为多样,包括顺式作用、反式作用和作为miRNA前体等(Ferrer and Dimitrova,2024)。顺式作用是指基因转录形成的lncRNA可以与基因组上蛋白编码基因的上下游基因启动子或共表达基因中的顺式作用元件相互作用,进而调控基因转录(Ferrer and Dimitrova,2024)。本研究发现,lncRNA5334通过顺式作用潜在调控Pol Ⅱ,Trx,ACS,GPDH等4个上下游基因。Pol Ⅱ介导的基因转录是真核生物基因组表达的第一步,也是真核生物发育、分化和对环境做出反应过程中细胞调控的焦点(Osman and Cramer,2020)。本研究中,Pol Ⅱ在2 dpi和3 dpi的表达量较之1 dpi上调,在4 dpi显著上调,总体表现为持续上升的表达趋势(图 3-A),与lncRNA5334的表达趋势相反。推测lncRNA5334通过顺式作用负调控Pol Ⅱ的转录,进而调节东方蜜蜂微孢子虫在宿主细胞中的增殖。Trx是一种高度保守的低分子量蛋白质,作为核苷酸还原酶的氢供体,在大肠杆菌Escherichia coli中被首次发现(Laurent et al.,1964)。有研究表明Trx在抗氧化防御机制、细胞增殖和细胞凋亡过程中发挥至关重要的作用(Yoshida et al.,2003;Jang and Van Remmen,2009;Said,2012)。Zhang等(2016)发现球孢白僵菌Beauveria bassiana的两种硫氧还蛋白还原酶(Trr1和Trr2)均定位于细胞质,且都能通过还原Trx主导细胞内的氧化还原状态,缺失Trr1后B. bassiana的6个Trx中的多数基因转录水平都发生上调,Trr1缺失可引起白僵菌产孢能力、孢子萌发、耐热性、紫外线抵抗力和毒性变化,而Trx1和Trx6的过表达能够逆转Trr1缺失造成的影响。本研究发现相比于1 dpi,Trx的表达水平在2 dpi,3 dpi和4 dpi皆显著上调,总体表现为先上升后下降的表达趋势(图 4-A)。这表明lncRNA5334可能通过顺式作用激活Trx转录进而动态调控东方蜜蜂微孢子虫侵染工蜂的过程。
ACS是细胞代谢中不可或缺的关键酶(Starai and Escalante-Semerena,2004;Li et al.,2019)。东方蜜蜂微孢子虫是一种专性的胞内真菌寄生虫且对宿主有着很强的能量依赖。Lei等(2022)对球孢白僵菌的BbAcs2蛋白进行功能分析,发现BbAcs2定位于过氧化物酶体且对胚芽中的脂质代谢、胚泡形成和毒力有显著影响。本研究中,ACS的表达水平在2 dpi和4 dpi均上调,在3 dpi显著上调,总体表现为先上升后下降的表达趋势(图 4-B),说明lncRNA5334可能通过顺式作用激活ACS转录进而调控东方蜜蜂微孢子虫在侵染过程中的毒力与代谢。GPDH催化甘油-3-磷酸的形成,在不同物种的甘油脂代谢和应对各种压力的过程中起到重要作用。有研究表明在渗透压的胁迫下酿酒酵母Saccharomyces cerevisiae的GPDH的活性上升,进而发挥调节渗透压的作用,此外GPDH还与酿酒酵母的甘油和酒精耐受性密切相关(Blomberg and Adler,1989)。GmGPDH12是一种来自大豆的线粒体FAD-GPDH,能通过调节氧化还原状态和呼吸来增加耐盐性和抗渗透胁迫性(Zhao et al.,2021)。本研究发现,东方蜜蜂微孢子虫的GPDH表达量在3 dpi和4 dpi被显著激活(图 3-B),推测东方蜜蜂微孢子虫在进入宿主体内后通过lncRNA5334调控GPDH的表达来适应宿主细胞内环境的压力。虽然本研究基于生物信息学分析和RT-qPCR检测结果发现lncRNA5334对Pol Ⅱ, Trx, ACS和GPDH具有潜在的顺式调控作用,但仍需要进一步的试验来证明。
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图 1 东方蜜蜂微孢子虫lncRNA5334扩增产物的琼脂糖凝胶电泳
注:泳道M,DNA marker;泳道N,未接种东方蜜蜂微孢子虫孢子的1日龄意大利蜜蜂工蜂中肠样品(阴性对照);泳道P,东方蜜蜂微孢子虫孢子样品(阳性对照);泳道1~4,东方蜜蜂微孢子虫接种后1~4 d的工蜂中肠样品。
Fig. 1 Agarose gel electrophoresis for the amplification products from lncRNA5334 in Nosema ceranae
Note: Lane M, DNA marker; lane N, The midgut sample from un-inoculated Apis mellifera ligustica 1-day-old worker (negative control); lane P, Nosema ceranae spore sample (positive control); lanes 1~4, The midgut samples from Apis mellifera ligustica worker at 1~4 days post inoculation with Nosema ceranae.
图 2 东方蜜蜂微孢子虫侵染意大利蜜蜂工蜂过程中lncRNA5334的相对表达量
注:图中数据为平均值±标准误;柱上不同字母表示差异显著(P < 0.05,Tukey氏检验)。下同。
Fig. 2 Determination of relative expression level of lncRNA5334 during Nosema ceranae's infection of Apis mellifera ligustica workers
Note: Data in the figure were mean ± SE; different letters above bars indicated significant difference (P < 0.05, Tukey's test). The same below.
表 1 本研究使用的引物序列
Table 1 Sequences of primers used in this study
名称Name 序列(5'-3') Sequence (5'-3') lncRNA5334-F GGCAGAATACTACGGCATA lncRNA5334-R ACACGGCTATTGTCCTTAG actin-F ACAATGGTTCAGGTATCGTA actin-R GTGCCTCATCTCCTACATAA Trx-F GGGATTTGGCATACTTCTA Trx-R CCCATATCATGTATTGTGTG ACS-F TGGCAGACAGAAACTGGTGGAA ACS-R GGTAAAGACGCACACTCAGGCT Pol Ⅱ-F AGAGAAAGAAACACATAGTCTTGGT Pol Ⅱ-R AGGATGGCATACTTTGTAAGAACT GPDH-F TGGTGTTACGGTTGGTCTAGGA GPDH-R GGCAATACCACACGACTGGAAT 表 2 LncRNA5334顺式调控的上下游基因概览
Table 2 Overview of upstream and downstream genes regulated by lncRNA5334 in a cis-acting manner
基因ID Gene ID Nr数据库注释Nr database annotation XM_024474896.1 Nosema ceranae thioredoxin family (AAJ76_270006410) XM_024476690.1 Nosema ceranae acetyl-coenzyme A synthetase (AAJ76_970005584) XM_024476687.1 Nosema ceranae DNA-directed RNA polymerase Ⅱ (AAJ76_970003904) XM_024476686.1 Nosema ceranae glycerol-3-phosphate dehydrogenase (AAJ76_970003126) -
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