陳二龍 范志勇 王松峰 王德勛 朱凱 孫軍偉 蘇家恩 宋朝鵬
摘 要:為探明煙草熱激蛋白70(Hsp70)基因家族的特征及煙葉主脈中NtHsp70Chl基因在烘烤條件下的表達(dá)模式,對(duì)Hsp70基因家族進(jìn)行了亞細(xì)胞定位、系統(tǒng)進(jìn)化、基因結(jié)構(gòu)、染色體定位,并對(duì)NtHsp70Chl基因進(jìn)行了烘烤條件下實(shí)時(shí)熒光定量表達(dá)PCR分析。結(jié)果表明,煙草基因組中Hsp70基因家族共有61個(gè)成員,蛋白序列長(zhǎng)度不等,等電點(diǎn)在4.52~9.75范圍內(nèi),各成員蛋白分別定位于細(xì)胞質(zhì)、內(nèi)質(zhì)網(wǎng)、細(xì)胞外基質(zhì)、葉綠體和線(xiàn)粒體中;煙草Hsp70基因家族分為6組,定位于葉綠體的成員均存在Ⅵ-a亞組;61個(gè)NtHsp70基因分布于18條染色體上,經(jīng)亞細(xì)胞定位于葉綠體的基因分別位于6、17和19號(hào)染色體上;煙草Hsp70家族中具有10個(gè)基因重復(fù)和5個(gè)旁系同源基因;經(jīng)RT-qPCR檢測(cè)分析,定位于煙草葉綠體中的NtHsp70Chl基因?qū)Ω邷卣T導(dǎo)的敏感性較弱。本研究為深入研究煙草Hsp70的功能奠定了基礎(chǔ)。
關(guān)鍵詞:煙草;主脈組織;Hsp70基因家族;生物信息學(xué);NtHsp70Chl;高溫誘導(dǎo)
中圖分類(lèi)號(hào):S572.03 文章編號(hào):1007-5119(2018)02-0008-09 DOI:10.13496/j.issn.1007-5119.2018.02.002
Bioinformatics of Tobacco(Nicotiana tabacum)Hsp70 Gene Family and Expression Analysis of NtHsp70Chl in Midrib
CHEN Erlong1, FAN Zhiyong2, WANG Songfeng3, WANG Dexun2, ZHU Kai2,
SUN Junwei2, SU Jiaen2, SONG Zhaopeng1*
(1. College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China 2; Dali Tobacco Company of Yunnan Province, Dali 671000, Yunnan, China; 3. Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of CAAS, Qingdao 266101, China)
Abstract: In order to study the relevant biological information of the tobacco heat shock protein 70 (Hsp70) gene family and the specific expression of the chloroplast-localized members NtHsp70Chl in tobacco midrib, subcellular location, system evolution, Gene structure, chromosome location, and real-time fluorescence quantitative expression PCR analysis were carried out. The results showed that 61 members of the tobacco Hsp70 gene family were identified. The numbers of amino acid contained in the protein sequence were different, and the isoelectric point was in the range of 4.52~9.75. And the protein members were predicted to be localized in the cytoplasm, endoplasmic Reticulum, extracellular matrix, chloroplast (4 members) and mitochondria respectively. The tobacco Hsp70 gene family was divided into 6 groups, and the NtHsp70Chl genes were all in the VI-a subgroup. 61 NtHsp70 genes are located on 18 chromosomes, and NtHsp70Chl genes were located on chromosomes 6, 17, and 19, respectively. In tobacco Hsp70 family, there are 10 duplications and 5 paralogous genes. According to RT-qPCR analysis, the NtHsp70Chl genes in tobacco midrib were weakly sensitive to high-temperature stress. This study laid the foundation for further exploration and application of tobacco Hsp70 functions.
Keywords: tobacco; midrib tissue; Hsp70 gene family; bioinformatics; NtHsp70Chl; high temperature induction
煙葉在烘烤過(guò)程中處于高溫和水分脅迫的環(huán)境[1]。Hsp70基因在高溫或干旱誘導(dǎo)的條件下表達(dá)量上調(diào),Hsp70蛋白參與蛋白質(zhì)的正確折疊,調(diào)節(jié)蛋白在細(xì)胞內(nèi)積累,增加組織的耐熱性[2-4]。葉綠體內(nèi)Hsp70蛋白可協(xié)助基質(zhì)中蛋白轉(zhuǎn)運(yùn),是必要的ATP酶,與類(lèi)囊體膜的形成和病原微生物入侵的嗜
基金項(xiàng)目:中國(guó)煙草總公司云南省公司項(xiàng)目“防治烘烤過(guò)程中煙葉腐爛霉變技術(shù)研究推廣”(2016YN10)、“返青寡日照等條件下難落黃煙葉的烘
烤技術(shù)研究及推廣”(2015YN20)
作者簡(jiǎn)介:陳二龍(1992-),男,碩士研究生,主要從事煙草調(diào)制加工研究。E-mail:celyctz@163.com。*通信作者,E-mail:ycszp@163.com
收稿日期:2017-07-22 修回日期:2017-11-17
好有一定關(guān)系[5-8]。
煙葉在烘烤過(guò)程中(逆境條件)進(jìn)行代謝活動(dòng),
且在一定程度上促進(jìn)病原微生物的入侵或擴(kuò)散,此時(shí),細(xì)胞內(nèi)一些抗性基因表達(dá)或上調(diào),如TLHS1、LFD、NPK1和Hsp70等[9-12]。Hsp70蛋白作為分子伴侶,其N(xiāo)端核酸結(jié)合域(NBD)與ATP/ADP相互作用,控制C端底物結(jié)構(gòu)域(SBD)以催化劑的形式調(diào)節(jié)蛋白質(zhì)的折疊和積累[13-14]。Hsp70基因家族成員的功能具有多樣性,如擬南芥中的AtHsp70-15在其植株的耐熱性方面發(fā)揮重要的作用[15],哈茨木霉菌的Hsp70基因通過(guò)轉(zhuǎn)基因表達(dá)使擬南芥對(duì)高溫以及非生物脅迫的抗性增加[16],斑茅在干旱脅迫的條件下,Hsp70基因表達(dá)量上調(diào),對(duì)調(diào)節(jié)細(xì)胞膜熱穩(wěn)定性和水分相對(duì)含量具有積極作用[17],部分植物體中Hsp70參與病原微生物的蛋白質(zhì)折疊等[18]。Hsp70的亞細(xì)胞位置可分為4類(lèi):內(nèi)質(zhì)網(wǎng)、細(xì)胞質(zhì)、線(xiàn)粒體及葉綠體[19]。目前,對(duì)植物Hsp70基因家族數(shù)據(jù)研究對(duì)象主要包括擬南芥[20]、胡楊[21]、水稻[22]、大豆[23]等,關(guān)于煙草Hsp70基因家族成員的研究較少。
研究煙草Hsp70基因家族成員的特征、進(jìn)化和表達(dá)模式,對(duì)于進(jìn)一步探討煙草中Hsp70基因家族的功能及指導(dǎo)煙葉的烘烤具有重要的作用。本研究在煙草全基因組的背景下,運(yùn)用生物信息學(xué)的方法挖掘煙草Hsp70基因家族的潛在信息,并以煙葉主脈組織內(nèi)NtHsp70Chl基因成員為研究對(duì)象,采用實(shí)時(shí)熒光定量表達(dá)探索其在熱激條件下的反應(yīng)。
1 材料與方法
1.1 材料
試驗(yàn)于2016年在云南省彌渡縣紅花大金元基地調(diào)制實(shí)驗(yàn)室進(jìn)行。
煙草(Nicotiana tabacum L)Hsp70基因家族的相關(guān)序列,下載于NCBI(https://www.ncbi. nlm.nih.gov/)和Sol Genomics Network(https:// solgenomics.net/)數(shù)據(jù)庫(kù)[24-25]。擬南芥的Hsp70蛋白序列來(lái)源于TAIR(http://www.arabidopsis.org/)和NCBI數(shù)據(jù)庫(kù)[26-27]。
煙草品種為紅花大金元,取樣地理位置為鳳儀鎮(zhèn)。取樣:(1)在常規(guī)烘烤(變黃前期干球/濕球溫度為35 ℃/35 ℃,烘烤時(shí)長(zhǎng)8 h,煙葉狀態(tài)為葉尖變軟;變黃中期38 ℃/37 ℃,32 h,葉片達(dá)到8黃;變黃后期42 ℃/36 ℃,16 h葉片9成黃)過(guò)程中,于烘烤0、12、24、36、48、60 h隨機(jī)取頂層煙葉3片,從主脈端口向下除去1 cm,以新端口為參照,向下取2 cm,去除兩側(cè)葉耳,將3條主脈混合包裹于錫箔紙中,放于液氮中并進(jìn)行標(biāo)記;(2)將適熟煙葉隨機(jī)裝于3組ZLKX-Ⅱ型煙葉烘烤箱(±0.5 ℃,鄭州智聯(lián)自動(dòng)化設(shè)備有限公司),第1組烘烤箱的溫濕度設(shè)定為35 ℃/35 ℃, 第2組設(shè)定為38 ℃/38 ℃, 第3組為42 ℃/42 ℃,期間的3組烘烤箱溫濕度設(shè)定均保持不變,在0、12和24 h進(jìn)行取樣,步驟同上。
1.2 煙草Hsp70基因家族的鑒定
利用已獲得擬南芥Hsp70基因家族的蛋白序列為比對(duì)文件[20],從上述數(shù)據(jù)庫(kù)中進(jìn)行BLAST(1e-10),將重復(fù)序列去除,并構(gòu)建本地?cái)?shù)據(jù)庫(kù);從Pfam(http://pfam.xfam.org/)數(shù)據(jù)庫(kù)獲得具有Hsp70結(jié)構(gòu)域的種子文件(PF00012)[28],通過(guò)HMMER3.0軟件搜索本地?cái)?shù)據(jù)庫(kù),確認(rèn)獲取的蛋白序列具有典型Hsp70結(jié)構(gòu)域。采用Protparam(http://us.expasy.org/tools/protparam.html)在線(xiàn)工具,預(yù)測(cè)煙草Hsp70的等電點(diǎn)、序列長(zhǎng)度及分子質(zhì)量[29]。煙草Hsp70的亞細(xì)胞定位的預(yù)測(cè)運(yùn)用ProtComp(http://linux1.softberry.com/berry.phtml? topic=protcomppl&group=programs&subgroup=proloc)工具進(jìn)行分析[30]。
1.3 煙草Hsp70基因的系統(tǒng)進(jìn)化分析
運(yùn)用ClustalW2軟件對(duì)煙草中61個(gè)Hsp70及擬南芥中已被確認(rèn)功能的Hsp70蛋白序列進(jìn)行比對(duì)[31];MEGA6軟件將比對(duì)結(jié)果進(jìn)一步分析轉(zhuǎn)化,生成進(jìn)化樹(shù),其構(gòu)建方式使用鄰接法(NJ)[32]。
1.4 煙草Hsp70基因的染色體定位和結(jié)構(gòu)分析
依據(jù)煙草Hsp70基因定位于染色體中的信息,采用Mapinspector 軟件呈現(xiàn)基因位于染色體中輪
廓圖[33];依據(jù)兩個(gè)基因的匹配長(zhǎng)度以及相似性是否大于80%判定基因復(fù)制,而基因是否處于同一染色 體中判定串聯(lián)復(fù)制或片段復(fù)制[34]。根據(jù)煙草Hsp70基因DNA和CDS序列的數(shù)據(jù),采用GSDS2(http://gsds.cbi.pku.edu.cn/)在線(xiàn)工具繪制基因結(jié)構(gòu)圖[35]。
1.5 煙草Hsp70基因的熒光定量表達(dá)分析
在亞細(xì)胞定位的結(jié)果中選擇定位于葉綠體的4個(gè)煙草Hsp70(NtHsp70Chl)基因,由于其相似性程度較高,特設(shè)計(jì)共用引物。將提取的RNA采用NanoDrop 2000分光光度計(jì)(Thermo Scientific,USA)(OD260/OD280)測(cè)定濃度,瓊脂糖凝膠電泳檢測(cè)RNA完整性,RNA逆轉(zhuǎn)錄試劑HiScript II Q RT SuperMix for qPCR由Vazyme公司生產(chǎn)(貨號(hào):R223-01)。依據(jù)基因序列信息,通過(guò)Roche LCPDS2軟件設(shè)計(jì)特異性引物,并由上海捷瑞生物工程有限公司合成,采用煙草L25作為內(nèi)參基因,熒光定量PCR引物和擴(kuò)增產(chǎn)物如表1。PCR使用的試劑盒為QuantiFast? SYBR? Green PCR Kit (Qiagen,Germany),并在熒光定量LightCycler? 480 Ⅱ型PCR儀(Roche,Swiss)上進(jìn)行反應(yīng)。PCR反應(yīng)程序:95 ℃ 5 min;95 ℃ 10 s,60 ℃ 30 s,40個(gè)循環(huán)。根據(jù)熔解曲線(xiàn)檢測(cè)擴(kuò)增產(chǎn)物特異性:從60 ℃緩慢升溫至97 ℃,每1 ℃采集5次熒光信號(hào)。依據(jù)2–ΔΔCT對(duì)數(shù)據(jù)進(jìn)行換算[36]。
2 結(jié) 果
2.1 煙草Hsp70家族成員信息
在煙草全基因組數(shù)據(jù)中檢索,分析獲得61個(gè)煙草Hsp70家族成員,依據(jù)各成員在染色體中的定位結(jié)果,依次對(duì)其進(jìn)行命名為NtHsp70-(1-61)。通過(guò)分析NtHsp70家族成員理化特性,等電點(diǎn)的范圍為4.52(NtHsp70-37)至9.75(NtHsp70-18);Hsp70蛋白序列最長(zhǎng)的為NtHsp70-60,由904個(gè)氨基酸組成,最短的序列為NtHsp70-32,由118個(gè)氨基酸組成。亞細(xì)胞定位結(jié)果表明,NtHsp70蛋白多定位于細(xì)胞質(zhì)及內(nèi)質(zhì)網(wǎng)中,其家族成員數(shù)量分別為25和23個(gè);6個(gè)家族成員定位于線(xiàn)粒體;4個(gè)家族成員(NtHsp70-19、NtHsp70-38、NtHsp70-41和NtHsp70-43)定位于葉綠體;僅3個(gè)家族成員定位于胞外基質(zhì)。NtHsp70家族成員的詳情信息見(jiàn)表2。
2.2 煙草Hsp70家族成員進(jìn)化與基因結(jié)構(gòu)分析
以煙草Hsp70基因家族的蛋白序列與擬南芥AtHsp70-1(CAB85987)、AtHsp70-2(CAB85986)、AtHsp70-3(AAF14038)、AtHsp70-4(BAB02269)、AtHsp70-5(AAF18501)、AtHsp70-6(CAB45063)、AtHsp70-7(BAA97012)、AtHsp70-8(AAD15393)、AtHsp70-9(CAB37531)、AtHsp70-10(CAB89371)、AtHsp70-11(AAF88019)、AtHsp70-12(BAB08435)、AtHsp70-13(AAB70400)、AtHsp70-14(AAG52240)、AtHsp70-15(AAG52244)、AtHsp70-16(AAD30257)、AtHsp70-17(CAB46039)和AtHsp70-18(AAG51503)的蛋白序列共同組建系統(tǒng)進(jìn)化樹(shù)(圖1)。篩選進(jìn)化樹(shù)獲得最終聚類(lèi)結(jié)果,依據(jù)拓?fù)浣Y(jié)構(gòu)及擬南芥家族組別劃分將其分為Ⅰ~Ⅵ組,其成員數(shù)分別為9、21、2、12、9、8個(gè)。Ⅰ、Ⅱ和Ⅲ組內(nèi)的蛋白質(zhì)主要定位于細(xì)胞質(zhì)(Ⅰ組NtHsp70-17和NtHsp70-22、Ⅱ組NtHsp70-18、NtHsp70-29、NtHsp70-39、NtHsp70-60和NtHsp70-61除外),Ⅳ和Ⅴ組成員主要位于內(nèi)質(zhì)網(wǎng)(Ⅴ組NtHsp70-8、NtHsp70-27、NtHsp70-30和NtHsp70-32除外),Ⅵ組中的蛋白定位于能量供應(yīng)細(xì)胞器中,其中Ⅵ-a亞組的NtHsp70成員定位于葉綠體,Ⅵ-b亞組成員位于線(xiàn)粒體;Ⅰ和Ⅴ組屬于Hsp110/SSE亞家族,Ⅱ、Ⅲ、Ⅳ、Ⅵ組屬于Dnak亞家族。NtHsp70具有5對(duì)旁系同源基因(NtHsp70-4/55、NtHsp70-19/38、NtHsp70-23/51、NtHsp70-33/34、NtHsp70-41/43)。Ⅰ組外顯子主要集中在5'端,Ⅱ組外顯子主要集中在3'端,Ⅲ組外顯子無(wú)內(nèi)含子或內(nèi)含子序列較短,Ⅳ組外顯子分散存在于3'端,Ⅴ和Ⅵ組的外顯子分布無(wú)明顯規(guī)律。
2.3 煙草Hsp70基因的染色體定位
為明確煙草Hsp70基因家族的組成與分布形式,依據(jù)其定位信息,制作染色體分布的信息圖(圖2)。煙草的24條染色體內(nèi)分布61個(gè)NtHsp70基因,其在染色體中的分布位置有所不同,多數(shù)分布于染色體的端部;每條染色體中的NtHsp70基因個(gè)數(shù)具有差異,2號(hào)染色體含有7個(gè)基因家族成員,其成員數(shù)目最多,9號(hào)染色體含有6個(gè)家族成員,15、21和24號(hào)染色體均包含5個(gè)家族成員,1、4、22和23號(hào)染色體均具有4個(gè)家族成員,7和19號(hào)染色體均有3個(gè)家族成員,5、6、14和17號(hào)染色體中有2個(gè)家族成員,8、11和18號(hào)染色體成員數(shù)最少,均為1個(gè)基因家族成員,于葉綠體中表達(dá)的基因分別位于6、17和19號(hào)染色體,目前3、10、12、13、16和20號(hào)染色體無(wú)任何NtHsp70基因家族成員信息。通過(guò)分析基因之間的關(guān)系,發(fā)現(xiàn)NtHsp70基因家族中共存在10個(gè)基因復(fù)制,分別為1組(NtHsp70-44至NtHsp70-48)基因簇、5對(duì)串聯(lián)重復(fù)(NtHsp70-10/11、NtHsp70-13/14、NtHsp70-36/37、NtHsp70-49/50、NtHsp70-58/59)和4對(duì)片段重復(fù)(NtHsp70-16/57、NtHsp70-20/42、NtHsp70-22/31、NtHsp70-28/52)?;蛑貜?fù)促進(jìn)煙草Hsp70家族成員擴(kuò)增。
2.4 NtHsp70Chl在煙草葉片主脈組織中的表達(dá)
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