陳軍 周平 王朝海 陸燚 梁振娟 王宗明 吳顯 李曉川
摘要:利用Clustal和MEGA 6程序進(jìn)行序列分析,建立了54個(gè)馬鈴薯糖轉(zhuǎn)運(yùn)子之間以及它們與其他物種中的同源蛋白的進(jìn)化關(guān)系。利用PLACE程序鑒定了42個(gè)糖轉(zhuǎn)運(yùn)子的順式調(diào)控元件。此研究結(jié)果有利于對(duì)馬鈴薯糖轉(zhuǎn)運(yùn)子加深理解,從而挑選出提高馬鈴薯經(jīng)濟(jì)性的位點(diǎn)。
關(guān)鍵詞:馬鈴薯;糖轉(zhuǎn)運(yùn)子;基因組;系統(tǒng)進(jìn)化關(guān)系;順式調(diào)控元件
中圖分類號(hào): S532.01文獻(xiàn)標(biāo)志碼: A
文章編號(hào):1002-1302(2020)08-0056-07
收稿日期:2019-03-25
基金項(xiàng)目:貴州省科技計(jì)劃(編號(hào):黔科合基礎(chǔ)[2019]1002)、黔科合基礎(chǔ)[2016]1003);現(xiàn)代農(nóng)業(yè)產(chǎn)業(yè)技術(shù)體系建設(shè)專項(xiàng)(編號(hào):CARS-10-ES23)。
作者簡(jiǎn)介:陳?軍(1971—),男,研究實(shí)習(xí)員,研究方向?yàn)轳R鈴薯遺傳育種。E-mail:jevenlee111@aliyun.com。
通信作者:李曉川,博士,研究實(shí)習(xí)員,研究方向?yàn)轳R鈴薯遺傳育種。E-mail:475383510@qq.com。
在先前的研究中,通過序列比對(duì)在馬鈴薯基因組中共鑒定出了54個(gè)糖轉(zhuǎn)運(yùn)蛋白基因[1],它們分別歸屬于8個(gè)基因家族,包括蔗糖轉(zhuǎn)運(yùn)蛋白(SUC或SUT)家族、糖轉(zhuǎn)運(yùn)蛋白(STP)家族、糖促進(jìn)蛋白(SFP)家族、多元醇/單糖轉(zhuǎn)運(yùn)蛋白(PMT)家族、肌醇轉(zhuǎn)運(yùn)蛋白(INT)家族、質(zhì)體葡萄糖轉(zhuǎn)運(yùn)蛋白(pGlcT)家族、液泡單糖轉(zhuǎn)運(yùn)蛋白(TMT)家族、液泡葡萄糖轉(zhuǎn)運(yùn)蛋白(VGT)家族。在本研究中,使用系統(tǒng)進(jìn)化分析的方法,在每個(gè)家族內(nèi),將馬鈴薯與其他植物的糖轉(zhuǎn)運(yùn)子進(jìn)行了對(duì)比進(jìn)化關(guān)系的分析。同時(shí),為了研究調(diào)控糖轉(zhuǎn)運(yùn)子基因的信號(hào)傳導(dǎo),也調(diào)查了它們的啟動(dòng)子序列,分析了位于啟動(dòng)子中的順式調(diào)控元件。
1?材料與方法
1.1?糖轉(zhuǎn)運(yùn)子基因的鑒定
鑒定的糖轉(zhuǎn)運(yùn)子基因,使用在地址https://blast.ncbi.nlm.nih.gov/Blast.cgi的BLASTp工具,以每個(gè)家族中馬鈴薯糖轉(zhuǎn)運(yùn)子的蛋白序列作為查詢序列,鑒定出各作物物種的糖轉(zhuǎn)運(yùn)子基因[2]。
1.2?多序列比對(duì)及系統(tǒng)進(jìn)化分析
將鑒定出來的糖轉(zhuǎn)運(yùn)子的氨基酸序列應(yīng)用Clustal Omega在線服務(wù)器(http://www.ebi.ac.uk/Tools/msa/clustalo/)進(jìn)行多序列比對(duì)[3]。進(jìn)化樹利用MEGA 6軟件的Neighbor-Joining參數(shù),經(jīng)過計(jì)算1 000次[4]。根據(jù)系統(tǒng)進(jìn)化分析將糖轉(zhuǎn)運(yùn)子基因劃分為不同的家族。
1.3?啟動(dòng)子序列分析
從馬鈴薯基因組中截取54個(gè)糖轉(zhuǎn)運(yùn)子基因上游2 kb的基因啟動(dòng)子序列,并利用植物啟動(dòng)子順式調(diào)控元件數(shù)據(jù)庫(PLACE:http://www.dna.affrc.go.jp/PLACE/index.html),搜索糖轉(zhuǎn)運(yùn)子基因啟動(dòng)子序列上的順式調(diào)控元件。
2?結(jié)果與分析
2.1?馬鈴薯糖轉(zhuǎn)運(yùn)子成員在其他植物中同源蛋白的系統(tǒng)進(jìn)化分析
2.1.1?蔗糖轉(zhuǎn)運(yùn)家族
3個(gè)馬鈴薯蔗糖轉(zhuǎn)運(yùn)蛋白特性都被較詳細(xì)地鑒定,它們定位于篩細(xì)胞的細(xì)胞膜[5-8](圖1-A)。SUT家庭成員確定為蔗糖和H+的協(xié)同轉(zhuǎn)運(yùn)子[9-11]。但特性各不相同,StSUT1對(duì)蔗糖有高親和力,但轉(zhuǎn)運(yùn)力較弱,StSUT4對(duì)蔗糖有低親和力,但轉(zhuǎn)運(yùn)力強(qiáng),同時(shí)StSUT4受光周期調(diào)控,而SUT2位于胞漿區(qū)的環(huán)狀結(jié)構(gòu)是糖的傳感器,受糖的誘導(dǎo)[5,12-13]。同時(shí),三者有形成聚合體的能力,三者可能聚合形成的寡聚體具有執(zhí)行蔗糖運(yùn)輸?shù)墓δ躘8]。
2.1.2?糖轉(zhuǎn)運(yùn)蛋白家族
除了來源于擬南芥中的STP外,一些茄科植物中的STP也被鑒定[14]。番茄STP命名為L(zhǎng)eHT1~LeHT3或SlSTP1~SlSTP3。SlSTP1和SlSTP2在酵母中是能量依賴性的葡萄糖轉(zhuǎn)運(yùn)蛋白[15-16]。5個(gè)馬鈴薯的STPs(StSTP1、StSTP2、StSTP3、StSTP15和StSTP16)與SlSTP1屬同一分支。它們與AtSTP1和VvHT1是在2個(gè)親緣關(guān)系很近的單獨(dú)分支(圖1-B)。AtSTP1是在酵母中顯示葡萄糖轉(zhuǎn)運(yùn)活性[17]?;诨虮磉_(dá)分析和原位雜交試驗(yàn)的基礎(chǔ)上,VvHT1被認(rèn)為在早期葡萄果實(shí)發(fā)育中運(yùn)輸己糖[18-19],而StSTP1在葉子和匍匐莖中表達(dá)量較高。
StSTP5同番茄、擬南芥、水稻和葡萄唯一的STP存在于一個(gè)單獨(dú)的分支。在這個(gè)分支中,VvHT5可能將碳水化合物供給到生物脅迫下的組織[20]。同樣,AtSTP13表達(dá)被認(rèn)為在真菌感染中與細(xì)胞程序性死亡是相關(guān)的[21]。當(dāng)AtSTP13過表達(dá)時(shí)還影響植物的生長(zhǎng)和氮含量[22]。而StSTP5在生物脅迫中表達(dá)水平顯著提高,暗示了它在其中的功能。
StSTP6、StSTP7和StSTP19同在酵母中沒有表現(xiàn)出糖運(yùn)輸活動(dòng)的SlSTP3、AtSTP7和VvHT3在同一分支[14,23-24]。蛋白質(zhì)StSTP8、StSTP17和StSTP20與VvHT4和AtSTP3形成一個(gè)單獨(dú)的分支。VvHT4在酵母中表達(dá)時(shí)表現(xiàn)出己糖轉(zhuǎn)運(yùn)活性[23]。AtSTP3是低親和力葡萄糖轉(zhuǎn)運(yùn)蛋白,可能還有其他己糖作為底物[25]。另一個(gè)分支是由StSTP9與OsMST1、AtSTP5和VvHT2組成。在酵母表達(dá)OsMST1和AtSTP5未見葡萄糖轉(zhuǎn)運(yùn)活性[26]。StSTP4同AtSTP4、AtSTP9和AtSTP11一起。在這個(gè)分支中,AtSTP9和AtSTP11分別在擬南芥花粉中顯示己糖轉(zhuǎn)運(yùn)活性[27-28]。其他擬南芥花粉特異性STP(AtSTP2和AtSTP6)與StSTP10-StSTP14以及StSTP18聚集在一起[29-30]。StSTP4、StSTP10、StSTP11以及StSTP12在RNA-seq數(shù)據(jù)庫中都在雄蕊中顯示較高水平的表達(dá)。
2.1.3?糖促進(jìn)蛋白家族
SFP家族的創(chuàng)始成員(AtERD6)在脫水和冷應(yīng)激過程中表達(dá),但缺乏轉(zhuǎn)運(yùn)活性的證據(jù)[31]。而StSFP6在熱脅迫下的相對(duì)表達(dá)水平有10倍的提高,提示StSFP6可能參與植物抗逆過程。在擬南芥中,AtSFP1和AtSFP2也沒有作為轉(zhuǎn)運(yùn)蛋白活性的證據(jù)[32]。最近,研究ERD6-like家族的另一名成員AtESL1,表明ERD6-like家族成員能促進(jìn)葡萄糖和一系列其他己糖的擴(kuò)散[33]。然而,沒有馬鈴薯的SFP蛋白(也沒有葡萄蛋白及番茄SFP蛋白)與這些擬南芥的SFP聚集在同一分支,暗示這些SFP在這些物種具有不同的功能(圖 1-C)。
2.1.4?多元醇/單糖轉(zhuǎn)運(yùn)蛋白
在擬南芥中,找到了6個(gè)PMT轉(zhuǎn)運(yùn)蛋白。AtPMT5在各種組織轉(zhuǎn)運(yùn)非特定的多元醇、己糖和戊糖轉(zhuǎn)運(yùn)(圖1-D)[34-35]。AtPMT1和AtPMT2轉(zhuǎn)運(yùn)木糖醇和果糖并在發(fā)育中的木質(zhì)部和花粉表達(dá)[36]。2種定位于韌皮部細(xì)胞膜的芹菜PMT蛋白被確定為甘露醇和H+的協(xié)同轉(zhuǎn)運(yùn)子,StPMT3和StPMT4與這兩者相近[37-38]。PcSOT1和PcSOT2發(fā)現(xiàn)在桃櫻(酸櫻桃)的儲(chǔ)存組織轉(zhuǎn)運(yùn)山梨醇[39]。在蘋果源葉的韌皮部,檢測(cè)到3種PMT(MdSOT3-MdSOT5)的表達(dá)[40]。在大車前(車前草)的韌皮部有2種PMT表達(dá)StPMT6與這2種PMT在同一分支[41]。
2.1.5?其他糖轉(zhuǎn)運(yùn)蛋白家族
肌醇轉(zhuǎn)運(yùn)蛋白是在冰葉日中花的單倍體中首次表征出來的[42]。隨后從擬南芥中鑒定出了3種INT基因。AtINT1編碼myo-肌醇轉(zhuǎn)運(yùn)蛋白并定位到液泡膜[43],而AtINT2和AtINT4則定位到細(xì)胞膜[44-45]。
在植物中,質(zhì)體定位的pGlcT首先在菠菜中被發(fā)現(xiàn),可能的作用是在夜間從葉綠體輸出淀粉分解產(chǎn)物[46]。最近也利用擬南芥基因敲除突變體AtpGlcT獲得了類似的結(jié)果[47]。可以推測(cè),降解的淀粉有利于果實(shí)含糖量。從質(zhì)體導(dǎo)出淀粉分解產(chǎn)物的能力讓pGlcT蛋白成為進(jìn)一步研究果實(shí)糖分積累的潛在蛋白[48]。在橄欖樹中,1個(gè)pGlcT型蛋白在果實(shí)發(fā)育期間表達(dá)[49]。馬鈴薯StpGlcT1發(fā)現(xiàn)與AtpGlcT及OepGlcT在同一分支,而StpGlcT1在成熟的果實(shí)中有高水平的表達(dá)。StpGlcT2被發(fā)現(xiàn)與OsGMST1序列相似度高,OsGMST1的敲除導(dǎo)致對(duì)高鹽條件的耐受性降低和略有減少葡萄糖和果糖的含量。在水稻中,OsGMST1被證明定位在高爾基體[50]。而AtSGB1作為G蛋白BETA1的抑制子與StpGlcT4有更高的相似性[51]。
到目前為止,已經(jīng)從擬南芥和水稻中鑒定出TMT。在擬南芥中,AtTMT1和AtTMT2定位在液泡膜,表現(xiàn)出葡萄糖或果糖/H+逆向運(yùn)輸?shù)鞍椎幕钚?,將糖輸入到液泡[52-54]。類似的結(jié)果也在水稻OsTMT1和OsTMT2中獲得[55]。但擬南芥TMT能在轉(zhuǎn)錄水平對(duì)環(huán)境刺激作出反應(yīng),如冷脅迫,而水稻TMT則沒有。
在擬南芥中只有一個(gè)VGT經(jīng)過鑒定[56]。在酵母和擬南芥原生質(zhì)體中,AtVGT1定位于液泡膜中證明具有向液泡中輸入葡萄糖的功能,并且在ATP供能下小程度地輸入果糖分到液泡中。
2.2?糖轉(zhuǎn)運(yùn)子基因轉(zhuǎn)錄調(diào)控的順式作用元件
從馬鈴薯基因組中截取54個(gè)糖轉(zhuǎn)運(yùn)子基因上游2 kb的基因啟動(dòng)子序列,但由于其他基因的ORF出現(xiàn)在糖轉(zhuǎn)運(yùn)子基因啟動(dòng)子區(qū)域內(nèi)或者由于測(cè)序結(jié)果的空缺(gap),有3個(gè)基因StSUT4(494個(gè)堿基對(duì))、StSFP4(756個(gè)堿基對(duì))和StINT1(1 417個(gè)堿基對(duì)),所得到的啟動(dòng)子序列短于2 kb。
經(jīng)過PLACE程序分析,得到的糖轉(zhuǎn)運(yùn)子的順式作用元件經(jīng)分類并用于比較。42種常見的順式調(diào)控元件,普遍存在于54個(gè)糖轉(zhuǎn)運(yùn)子的啟動(dòng)子區(qū)域,其中16種順式調(diào)控元件存在于所有糖轉(zhuǎn)運(yùn)子的啟動(dòng)子,4種順式調(diào)控元件(BIHD1OS、EBOXBNNAPA、MYCCONSENSUSAT和WBOXATNPR1)只在3個(gè)較短的基因啟動(dòng)子(StSUT4、StSFP4和StINT1)中缺失,6種順式調(diào)控元件只在1個(gè)基因啟動(dòng)子中缺失(表1)。
此外,有些順式序列(如DOFCOREZM)高度重復(fù),在54個(gè)基因的啟動(dòng)子區(qū)域顯示多達(dá)1 937份。這些共同的順式作用元件能在不同的植物器官影響基因表達(dá),如葉,芽,根,種子和花(花粉)。它們還響應(yīng)以不同的植物激素(脫落酸、赤霉素、乙烯、細(xì)胞分裂素),以及對(duì)許多環(huán)境因素(光、二氧化碳,生物和非生物脅迫),主要是存在于葉片和芽的多個(gè)順式作用元件序列(EBOXBNNAPA、GATABOX、GT1CONSENSUS、GTGANTG10、IBOXCORE)需要通過光進(jìn)行轉(zhuǎn)錄調(diào)控,這與糖轉(zhuǎn)運(yùn)子在光合作用器官和儲(chǔ)存器官之間轉(zhuǎn)運(yùn)糖是一致的。
3?結(jié)論
在本研究中,利用之前鑒定得到的54個(gè)糖轉(zhuǎn)化蛋白,利用系統(tǒng)進(jìn)化分析的方法,在每個(gè)家族內(nèi),將馬鈴薯與其他植物的糖轉(zhuǎn)運(yùn)子進(jìn)行了對(duì)比進(jìn)化關(guān)系的分析,分析了與糖轉(zhuǎn)化蛋白序列類似的蛋白功能。同時(shí),研究了調(diào)控糖轉(zhuǎn)運(yùn)子基因的信號(hào)傳導(dǎo),調(diào)查了它們的啟動(dòng)子序列,分析了位于啟動(dòng)子中的順勢(shì)調(diào)控元件,以期為下一步分析糖轉(zhuǎn)運(yùn)子的具體功能提供理論基礎(chǔ)。
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