楊會曉 孫媛媛 賈彩紅 金志強 徐碧玉 王卓
摘 ?要??苯丙氨酸解氨酶(Phenylalanine ammonia-lyase, PAL)是催化苯丙烷代謝途徑第1步反應(yīng)的限速酶,廣泛地參與植物生長發(fā)育過程中的各種生理活動。本研究通過生物信息學分析,從香蕉A基因組數(shù)據(jù)庫中利用BLASTp篩選出53個可能的MaPAL編碼蛋白序列。在NCBI分析蛋白保守結(jié)構(gòu)域,發(fā)現(xiàn)僅有8個基因具有典型的PAL家族基因的特性。聚類分析結(jié)果表明香蕉MaPAL家族的8個基因可以分為Class I 和Class II兩類。轉(zhuǎn)錄組數(shù)據(jù)表明,所有MaPAL基因在果實發(fā)育階段高表達,MaPAL5參與果實采后成熟過程。在干旱、低溫、鹽處理的香蕉幼苗葉片中,MaPAL1、MaPAL2、MaPAL3、MaPAL4和MaPAL5成員均顯著上調(diào)表達,MaPAL6號成員顯著下調(diào)表達,這些成員參與香蕉響應(yīng)上述非生物脅迫過程。8個MaPAL成員在枯萎病菌處理下均顯著下調(diào)表達,表明在感病品種巴西蕉根系中,MaPAL基因的表達全部被Foc TR4抑制。本研究結(jié)果為分析MaPAL基因家族在香蕉果實品質(zhì)形成和響應(yīng)逆境中的作用提供了理論依據(jù)。
關(guān)鍵詞 ?香蕉;苯丙氨酸解氨酶;系統(tǒng)進化分析;表達分析;基因家族中圖分類號??S668.1??????文獻標識碼??A
Identification and Expression Analysis of Phenylalanine Ammonia-lyase Gene Family in Banana
YANG Huixiao1,2, SUN Yuanyuan1,2, JIA Caihong1, JIN Zhiqiang1,2, XU Biyu1, WANG Zhuo1*
1. Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences / Key Laboratory of Tropical Biotechnology, Ministry of Agriculture and Rural Affairs, Haikou, Hainan 571101, China; 2. College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
Abstract ?Phenylalanine ammonia-lyase gene (PAL) is one of the key enzymes associated with plant growth and stress resistance in the secondary metabolism pathway. In this study, we used four L-phenylalanine ammonia-lyase genes inArabidopsis thalianaas qurry and acquired 53 candidate PAL gene sequences by BLASTp in banana A genome database. And then we used conserved domain search of NCBI, only 8 gene members were found containing?typical PAL domain in the protein sequence. In?the?phylogenetic tree, eight?PALs could be classified into 2 groups, Class I and Class II. The transcriptome data showed that allMaPALgenes were highly expressed at fruit development stages. AndMaPAL5was differential expression in banana fruit postharvest stages. Under the drought, low temperature and salt stresses,MaPAL1,?MaPAL2,MaPAL3,MaPAL4andMaPAL5members were up-regulated andMaPAL6was?down-regulated. All 8MaPALswere down-regulated under the Foc TR4 infection. The results suggested that allMaPAL genes played?important roles in banana fruit development and ripenning, responding to abiotic and biotic stresses. This study would provide a theoretical basis for further exploration the function of MaPALs?in banana fruit ripening and under stresses.
Keywords ?banana; phenylalanine ammonia-lyase; phylogenetic analysis; expression analysis; gene family
DOI10.3969/j.issn.1000-2561.2019.10.007
香蕉是多年生草本植物,是重要的熱地亞熱帶經(jīng)濟作物。其果實富含淀粉和黃酮類物質(zhì),是人們重要的糧食和營養(yǎng)來源[1]。在香蕉生長過程中,幼苗會經(jīng)常受到各種非生物和生物脅迫的影響,如干旱、低溫、鹽[2-3]和枯萎病[4],嚴重地影響香蕉果實的產(chǎn)量和品質(zhì)。尤其是香蕉枯萎病,由于抗病育種無法滿足香蕉產(chǎn)業(yè)的需求,且沒有有效的化學防治手段,造成香蕉栽培面積不斷地減少[5]。在香蕉中,次級代謝物質(zhì)與果實的品質(zhì)形成、抗非生物脅迫和抗枯萎病的關(guān)系密切[6-7]。苯丙氨酸解氨酶(phenylalanine ammonia-lyase, PAL, EC 4.3.1.5)催化保守的L-苯丙氨酸轉(zhuǎn)化為反式肉桂酸,它是苯丙烷類代謝的第一個關(guān)鍵酶和限速酶[8]。PAL蛋白廣泛存在于植物、真菌、酵母和藻類中。在植物基因組中,PAL編碼1個小的多基因家族,分子量一般在220~330 ku,是一種酸性蛋白[9]。在植物中,多種次級代謝產(chǎn)物如花青素、木質(zhì)素、激素、類黃酮和植物抗毒素等的合成都是源于苯丙烷類合成途徑,PAL是該途徑的第一個關(guān)鍵酶[10]。PAL基因的表達受各種環(huán)境脅迫的影響,如病原菌侵染、紫外線、傷害和光照等的誘導[11-12]。此外,PAL在植物防御系統(tǒng)中起著重要作用,參與信號分子水楊酸的生物合成,水楊酸是植物系統(tǒng)獲得抗性所必需的有機酸[13-14]。截至目前,PAL基因在多種植物中被發(fā)現(xiàn),例如葡萄(Vitis vinifera L.)[15]、大豆(Glycine max (Linn.) Merr.)[16]、陸地棉(Gossypium hirsutum Linn.)[17]、甜瓜(Cucumis meloL.)[18]、玉米(Zea maysL.)[19]、蘋果((Malus?domestica)[20]、沙棘(Hippophae rhamnoidesLinn.)[21]和核桃(Juglans regia L.)[22]等。在香蕉中,前期研究發(fā)現(xiàn)PAL參與香蕉果實抗冷[23],抗Mycosphaerella fijiensis侵染[24];在香蕉感染枯萎病菌后,PAL酶活性升高,且與香蕉的抗病性呈正相關(guān)[25]。截至目前,在香蕉中還未見PAL基因家族的全基因組分析的報道。
香蕉A基因組測序于2012年完成并公布測序結(jié)果[26],為在全基因組水平上對PAL基因家族進行分析鑒定、進化分析以及相關(guān)基因功能研究提供了數(shù)據(jù)支持。本研究通過生物信息學方法研究香蕉全基因組中的PAL基因家族的分類、系統(tǒng)進化關(guān)系、基因結(jié)構(gòu)、基因表達等,以期明確PAL基因家族在香蕉果實發(fā)育和采后成熟,響應(yīng)非生物和生物脅迫中可能發(fā)揮的作用,為深入研究香蕉苯丙氨酸解氨酶的功能奠定理論基礎(chǔ)。
1.1材料
以文獻報道的擬南芥4個PAL的數(shù)據(jù)[27],在擬南芥數(shù)據(jù)庫(http://www.arabidopsis.org/)中下載AtPAL的蛋白序列。以搜索到的擬南芥的AtPAL蛋白序列為查詢序列(Query),在香蕉A基因組數(shù)據(jù)庫(http://banana-genome.cirad.fr/)中,通過Blastp 搜索出香蕉的可能的PAL蛋白序列和相關(guān)基因注釋文件。
1.2方法
1.2.1 ?香蕉PAL基因的氨基酸序列屬性分析??利用ExPASy Proteomics Server(http://www.?expasy.org/)的ProtParam tool軟件在線分析蛋白的基本理化性質(zhì),包括蛋白的等電點、不穩(wěn)定系數(shù)、分子量、脂肪指數(shù)和疏水性等。采用Plant-mPLoc Server (http://www.csbio.sjtu.edu.cn/bioinf/?plant-?multi/#)在線預測分析MaPAL蛋白亞細胞定位情況。利用Gene Structure Display Server(GSDS)[28]軟件分析內(nèi)含子和外顯子組成。
利用DNAMAN軟件對MaPAL蛋白進行多重序列比對,依據(jù)比對結(jié)果鑒定MaPAL基因的旁系同源對[29]。旁系同源對基因必須滿足以下2個條件:(1)2個基因序列比對,短基因序列與長基因序列的覆蓋率大于70%;(2)2個基因蛋白序列的一致性大于70%[30]。
80DAF-0DPH(斷蕾80?d-采后成熟0?d),8DPH(采后成熟8 d)、14DPH(采后成熟14 d)進行了轉(zhuǎn)錄組分析(圖4)。MaPAL1、MaPAL2、MaPAL3、MaPAL6、MaPAL7和MaPAL8在果實發(fā)育階段(0DAF、20DAF)表達量較高;但這些成員在果實采后成熟階段幾乎不表達。MaPAL4基因在果實發(fā)育和采后成熟2個階段一直是高水平表達(RPKM>10),而且該成員在采后的表達達到顯著差異表達(Log2RPKM>1),表明該成員可能在香蕉果實發(fā)育和采后成熟中起著重要作用。MaPAL5在果實發(fā)育和采后成熟過程都不表達,表明該成員可能不參與香蕉果實發(fā)育和采后成熟過程。
2.4MaPAL在香蕉響應(yīng)脅迫處理的表達分析
如圖5所示,在低溫處理條件下,MaPAL1、MaPAL3、MaPAL4、MaPAL5、MaPAL7和MaPAL8顯著上調(diào)表達;MaPAL2和MaPAL6顯著下調(diào)表達。在干旱條件下,MaPAL3、MaPAL4、MaPAL1、MaPAL5和MaPAL7顯著上調(diào)表達,MaPAL2、MaPAL6和MaPAL8顯著下調(diào)。在鹽脅迫下,MaPAL2、MaPAL3、MaPAL4、MaPAL1、MaPAL5、MaPAL7和MaPAL8顯著上調(diào)表達,MaPAL6顯著下調(diào)表達。在3種非生物脅迫條件下,我們發(fā)現(xiàn)MaPAL3、MaPAL4、MaPAL5、MaPAL1、MaPAL7和MaPAL6均顯著上調(diào)和下調(diào),參與香蕉響應(yīng)上述3種非生物脅迫。在枯萎病處理中,所有8個MaPAL基因全部下調(diào)表達,其中MaPAL5下調(diào)最明顯。表明巴西蕉在遭受Foc TR4侵染后,全面抑制了MaPAL基因的表達。上述結(jié)果也表明PAL基因家族成員參與香蕉響應(yīng)逆境的過程。
PAL是連接初級代謝和苯丙烷類代謝、催化苯丙烷類代謝途徑第一步反應(yīng)的酶,是苯丙烷類代謝的關(guān)鍵酶和限速酶,苯丙烷類代謝途徑的產(chǎn)物在植物生長發(fā)育和響應(yīng)逆境過程中發(fā)揮著重要作用[33]。本研究對香蕉基因組中的PAL基因進行鑒定,并且進一步探討了MaPAL蛋白的理化性質(zhì)、基因結(jié)構(gòu)、系統(tǒng)進化關(guān)系及其在果實發(fā)育、采后成熟、響應(yīng)非生物和生物脅迫中的表達模式。本文在香蕉A基因組中共鑒定出8個MaPAL基因,與水稻(9個)[34]、楊樹(5個)[35]和擬南芥(4個)[36]基因組中的PAL數(shù)量相差不大,表明PAL在植物中確實以小基因家族的形式存在[37-38]。在氨基酸長度、分子量及等電點方面8個MaPAL都與其他植物的PAL蛋白類似[39-41]。理化性質(zhì)分析結(jié)果顯示,8個MaPAL都是酸性蛋白質(zhì),與之前報道的PAL是一種酸性蛋白的結(jié)果一致[42]。序列比對發(fā)現(xiàn),MaPAL結(jié)構(gòu)高度保守,都含有1個由Ala-Ser-Gly組成的高度保守的亞甲基咪唑酮(MIO)親電基團[43],這是PAL基因家族的特征序列。本研究預測所有的PAL均位于細胞質(zhì)類,與前人的報道一致[37, 44],說明香蕉PAL基因在細胞質(zhì)內(nèi)發(fā)揮作用。在進化方面,MaPAL基因能分為兩類,其中MaPAL1、MaPAL2、MaPAL3、MaPAL4、MaPAL5、MaPAL7和MaPAL8分為一個亞支,這些成員間具有較高的同源性;而MaPAL6單獨與其他木本植物的PAL分為一亞支。這與其他物種結(jié)果類似[45]。上述特征表明MaPAL1~8確實屬于香蕉PAL基因家族的成員。
果實的發(fā)育和成熟過程是香蕉品質(zhì)形成的重要過程。次級代謝物質(zhì)在該過程大量生成和轉(zhuǎn)化[6]。PAL作為苯丙烷代謝和類黃酮生物合成途徑的關(guān)鍵酶,在植物的發(fā)育過程中起著關(guān)鍵作用,覆盆子[46]和蘋果[20]的PAL均參與果實的發(fā)育過程。本研究發(fā)現(xiàn)在果實發(fā)育過程中大部分的MaPAL基因都表達量較高,說明次級代謝物質(zhì)的合成在這些香蕉果實發(fā)育時間點是很活躍的。而在果實采后成熟過程中MaPAL4成員高表達且顯著差異表達,說明這個成員可能在采后成熟過程中起著重要作用。
植物在遭受干旱、低溫和鹽等非生物學脅迫時,會迅速積累ROS,造成氧化損傷[47]。類黃酮等物質(zhì)在苯丙烷代謝途徑中合成,具有較強的抗氧化活性,能清除ROS,保護植物。在植物遭受逆境因素(如高溫、鹽害、紫外線等)均能促使PAL基因表達量變化;番茄[48]、黃瓜[49]和半夏[50]的PAL基因在非生物脅迫中顯著上調(diào)表達[51]。本研究發(fā)現(xiàn),大部分的MaPAL基因都參與香蕉響應(yīng)低溫、干旱和鹽的脅迫;其中有5個成員以相同的方式響應(yīng)上述3種非生物脅迫處理,表明MaPAL參與香蕉響應(yīng)非生物脅迫過程,且在功能上可能具有一定的冗余,這與擬南芥4個PAL結(jié)果類似[27]。
PAL基因參與植物響應(yīng)病原菌過程[8,24,?52-53],PAL酶活往往作為植物抗病的標志酶[25]。在擬南芥中,pal1/pal2/pal3/pal4的4敲除突變體表現(xiàn)發(fā)育不良和不育的表型,同時易感丁香假單胞菌(Pseudomonas syringae)[27]。巴西蕉作為香蕉的主要栽培品種,易感枯萎病[4-5]。本研究中,接種枯萎病的巴西蕉根系中MaPAL基因的表達顯著被抑制(圖5),說明MaPAL基因參與香蕉響應(yīng)枯萎病菌侵染的過程。酚酸類物質(zhì)參與香蕉抗枯萎病的過程[7],在感病品種中抑制MaPAL基因的表達可以減少次級代謝物質(zhì)的合成,影響抗病物質(zhì)的合成。上述結(jié)果說明MaPAL基因可能在香蕉抗枯萎病中起著重要作用。
基于香蕉A基因組的序列信息,獲得8個MaPAL家族成員信息, 并完成系統(tǒng)進化分析。MaPAL家族基因在果實發(fā)育時期表達量較大, 而在果實成熟中只有MaPAL4差異表達;在響應(yīng)非生物脅迫時,大部分MaPAL成員都參與香蕉響應(yīng)低溫、干旱和鹽脅迫的過程;8個MaPAL基因在感病香蕉品種接種Foc TR4后表達均被抑制。說明MaPAL基因在香蕉響應(yīng)逆境中起著重要作用。本研究結(jié)果為今后在香蕉中開展MaPAL調(diào)控次級代謝物質(zhì)合成的遺傳調(diào)控研究奠定了基礎(chǔ)。
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