Comparative proteomics of two Populus spp.(Section Tacamahaca) allotriploid derived by different types of 2n female gamete and their parents
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摘要:目的研究两种2n雌配子来源的青杨杂种三倍体与亲本的蛋白质组表达差异，从蛋白水平探讨异源三倍体杨树在生长、抗性等方面具有优势的分子基础，为杨树多倍体选育和遗传改良提供科学依据。方法采用同位素标记相对和绝对定量(iTRAQ)技术对青杨三倍体与其亲本进行定量蛋白质组学研究，所提取的杨树蛋白质样品经FASP酶解、iTRAQ试剂标记、高pH-RPLC分离、RPLC-MS分离分析，获取的串联质谱数据通过软件Proteome Discoverer 1.3搜库进行蛋白质鉴定，通过蛋白质相对定量的比较寻找差异表达蛋白，再对差异蛋白质进行GO、KEGG代谢通路分析。结果本研究共鉴定出1 472个蛋白质，差异蛋白202个。FDR和SDR青杨杂种三倍体与母本‘哲引3号杨’、父本‘北京杨’的差异蛋白比率在2.0%~10.1%之间。两种不同2n配子来源三倍体中FDR与亲本差异蛋白比率最高，且两种三倍体与父本的差异蛋白比率均比母本高。通路注释分析显示，差异蛋白显著富集于代谢相关、核糖体组装、光合作用和胁迫响应等通路。结论杂交和加倍后促进了蛋白质的合成以及光合作用的增强，并提高了多倍体的抗逆性和适应性，这些变化促进了杨树异源多倍体营养生长优势的形成。Abstract:ObjectiveAlthough Populus allotriploid has a prominent vegetative growth advantages, the underlying molecular mechanisms have not yet been revealed and elucidated. This work was designed to investigate proteins differentially expressed in the two Populus allotriploid derived by different types of 2n female gamete and their parents. The results will provide the scientific foundation for Populus polyploidy selection and genetic improvement.MethodThe iTRAQ proteomics approach was used in this study. The extracted proteins were digested using FASP method and identified by iTRAQ coupled with LC-MS/MS technology. Raw data were analyzed by Proteome Discoverer 1.3 search engine. Then the pathway analysis was conducted using GO and KEGG.ResultA total of 1 472 proteins were identified and 202 proteins were detected as differentially expressed proteins. The ratio of differentially expressed proteins between FDR and SDR Populus allotriploid and the two parents varied from 2.0% to 10.1%. Compared with the female parent or male parent, the ratio of differentially expressed proteins in FDR Populus allotriploid was higher than in SDR Populus allotriploid. In particular, there was an expression level dominance bias toward the triploid progenitors. Further analysis showed that the differentially expressed proteins were significantly enriched in the pathways such as metabolic related, ribosomes, photosynthesis and response to stress.ConclusionThe results indicated that plyploidization and hybridization could enhance photosynthesis, proteins synthetic and increased the resistance and adaptability of Populus polyploidy. All of these contribute to vegetative growth advantages in allotriploid plants.
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Keywords:
- 2n female gamete /
- Populus allotriploid /
- proteomics /
- iTRAQ
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图 1 两种青杨杂种三倍体子代与亲本差异蛋白维恩图分析
Figure 1. Venn diagrams of proteins differentially expressed in two Populus allotriploid and diploid parents
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图 2 FDR青杨杂种三倍体与二倍体亲本差异蛋白GO功能分类
PO.光呼吸作用；OR.氧化还原过程；LC.脂质代谢过程；RC.镉离子响应；G.糖酵解；HP.过氧化氢分解代谢过程；DR.对细菌的防御反应；ET.电子传递链；NR.催化活性的负调控；MC.单酰甘油分解代谢过程；DP.二酰甘油代谢过程；PN.嘌呤核苷酸转运；RG.呼吸气体交换；GC.甘氨酸分解代谢过程；CP.叶绿素生物合成过程；OA.氧化还原酶活性；HA.水解酶活性；CE.羧酸酯水解酶活性；PER.过氧化物酶活性；CO.辅酶结合；CI.铜离子结合；AO.替代氧化酶活性；AL.酰基甘油脂肪酶活性；AT.ATP：ADP逆向转运蛋白活性；FR.果糖二磷酸醛缩酶活性；NA.NADH脱氢酶(泛醌)活性；DO.δ4-3-氧代甾族5β-还原酶活性；PEP.肽酶活性；ER.烯酮还原酶活性；EI.内肽酶抑制剂活性；CT.叶绿体类囊体；RE.呼吸链；CW.细胞壁；CH.叶绿体包膜；CY.细胞溶质；EX.细胞外区域；AP.质外体；CM.叶绿体类囊体膜；MI.线粒体内膜；RCC.呼吸链复合体Ⅰ；MRC.线粒体呼吸链复合体Ⅰ；CHL.叶绿体；ME.线粒体被膜；MM.线粒体膜；TH.类囊体；TR.翻译；RB.核糖体生物合成；RM.RNA甲基化；CBP.香豆素生物合成过程；RS.盐胁迫响应；PMP.苯丙素类代谢过程；GO.高尔基组织；CMA.细胞修饰氨基酸生物合成过程；SB.S-腺苷甲硫氨酸生物合成过程；WT.水分运输；RH.根毛伸长；PBP.苯丙素类生物合成过程；RHL.激素水平调节过程；SC.核糖体的组成结构；RR. rRNA结合；RN. RNA结合；SCC.细胞骨架的结构成分；MA.甲硫氨酸腺苷转移酶活性；SMA.结构分子活性；PAP.苯丙氨酸解氨酶活性；ALA.氨解酶活性；HY.水解酶活性、作用于酯键；GT.谷胱甘肽转移酶活性；RIB.核糖体结合；3D.3-脱氧-7磷酸庚酮酸合酶活性；RIC.核糖核蛋白复合体；RI.核糖体；CL.胞质大核糖体亚基；CR.细胞质核糖体；IN.细胞内；P.胞间连丝；CS.细胞质小核糖体亚基；NU.核仁；GOA.高尔基体；CYT.细胞质；LR.大亚基。下同。
Figure 2. GO analysis of proteins differentially expressed in FDR Populus allotriploid and the diploid parents
PO, photorespiration; OR, oxidation-reduction process; LC, lipid catabolic process; RC, response to cadmium ion; G, glycolysis; HP, hydrogen peroxide catabolic process; DR, defense response to bacterium; ET, electron transport chain; NR, negative regulation of catalytic activity; MC, monoacylglycerol catabolic process; DP, diacylglycerol catabolic process; PN, purine nucleotide transport; RG, repiratory gaseous exchange; GC, glycine catabolic process; CP, chlorophyll biosynthesis process; OA, oxidoreductase activity; HA, hydrolase activity acting on ester bonds; CE, carboxylic ester hydrolase activity; PER, peroxidase activity; CO, coenzyme binding; CI, copper ion binding; AO, alternative oxidase activity; AL, acylglycerol lipase activity; AT, ATP:ADP antiporter activity; FR, fructose-bisphosphate aldolase activity; NA, NADH dehydrogenase (ubiquinone) activity; DO, delta4-3-oxosteroid 5beta-reductase activity; PEP, peptidase activity; ER, enone reductase activity; EI, endopeptidase inhibitor activity; CT, chloroplast thylakoid; RE, respiratory chain; CW, cell wall; CH, chloroplast envelope; CY, cytosol; EX, extracellular region; AP, apoplast; CM, chloroplast thylakoid membrane; MI, mitochondrial inner membrane; RCC, respiratory chain complex Ⅰ; MRC, mitochondrial respiratory chain complex Ⅰ; CHL, chloroplast; ME, mitochondrial envelope; MM, mitochondrial membrane; TH, thylakoid; TR, translation; RB, ribosome biogenesis; RM, RNA methylation; CBP, coumarin biosynthetic process; RS, response to salt stress; PMP, phenylpropanoid metabolic process; GO, Golgi organization; CMA, cellular modified amino acid biosynthetic process; SB, S-adenosylmethionine biosynthetic process; WT, water transport; RH, root hair elongation; PBP, phenylpropanoid biosynthetic process; RHL, regulation of hormone levels; SC, structural constituent of ribosome; RR, rRNA binding; RN, RNA binding; SCC, structural constituent of cytoskeleton; MA, methionine adenosyltransferase activity; SMA, structural molecule activity; PAP, phenylalanine ammonia-lyase activity; ALA, ammonia-lyase activity; HY, hydrolase activity, acting on ester bonds; GT, glutathione transferase activity; RIB, ribosome binding; 3D, 3-droxy-7-phosphoheptulona; RIC, ribonucleoprotein complex; RI, ribosome; CL, cytosolic large ribosomal subunit; CR, cytosolic ribosome; IN, intracellular; P, plasmodesma; CS, cytosolic small ribosomal subunit; NU, nucleolus; GOA, Golgi apparatus; CYT, cytoplasm; LR, large ribosomal subunit. The same below.
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图 3 SDR青杨杂种三倍体与二倍体亲本差异蛋白GO功能分类
PRO.蛋白水解；REC.冷响应；LM.脂质代谢过程；PF.类黄酮生物合成过程的正调控；LO.脂质氧化；RW.对伤害的反应；CRB.叶绿体二磷酸核酮糖羧化酶复杂的生物发生；SPA.丝氨酸型肽酶活性；SE.丝氨酸型内肽酶活性；LLA.亚油酸酯13S-脂氧合酶活性；OAA.氧化还原酶活性，作用于具有掺入分子氧的单个供体；UDP.UDP-葡糖基转移酶活性；RCA.核酮糖二磷酸羧化酶活性；LAL.长链脂肪酸-CoA连接酶活性；AEA.醛糖1-差向异构酶活性；CHR.叶绿体二磷酸核酮糖羧化酶复合物；PCW.植物型细胞壁；CMP.碳水化合物代谢过程；LB.木质素生物合成过程；RO.氧化应激反应；OM.单碳代谢过程；GR.生长；AGA. 4-α-葡聚糖转移酶活性；DA.二磷酸果糖-6-磷酸1-磷酸转移酶活性；GH.甘氨酸羟甲基转移酶活性；DL.UDP-葡萄糖醛酸脱羧酶活性；CHS.叶绿体基质。下同。
Figure 3. GO analysis of proteins differentially expressed in SDR Populus allotriploid and diploid parents
PRO, proteolysis; REC, response to cold; LM, lipid metabolic process; PF, positive regulation of flavonoid biosynthetic process; LO, lipid oxidation; RW, response to wounding; CRB, chloroplast ribulose bisphosphate carboxylase complex biogenesis; SPA, serine-type peptidase activity; SE, serine-type endopeptidase activity; LLA, linoleate 13S-lipoxygenase activity; OAA, oxidoreductase activity, acting on single donors with incorporation of molecular oxygen; UDP, UDP-glucosyltransferase activity; RCA, ribulose-bisphosphate carboxylase activity; LAL, long-chain fatty acid-CoA ligase activity; AEA, aldose 1-epimerase activity; CHR, chloroplast ribulose bisphosphate carboxylase complex; PCW, plant-type cell wall; CMP, carbohydrate metabolic process; LB, lignin biosynthetic process; RO, response to oxidative stress; OM, one-carbon metabolic process; GR, growth; AGA, 4-alpha-glucanotransferase activity; DA, diphosphate-fructose-6-phosphate 1-phosphotransferase activity; GH, glycine hydroxymethyltransferase activity; DL, UDP-glucuronate decarboxylase activity; CHS, chloroplast stroma. The same below.
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图 4 FDR和SDR青杨杂种三倍体与二倍体亲本差异蛋白KEGG通路分析
PB.苯丙素生物合成；PM.苯丙氨酸代谢；GD.乙醛酸和二羧酸代谢；APM.精氨酸和脯氨酸代谢；NM.氮代谢；FB.类黄酮生物合成；LA.亚油酸代谢；PC.卟啉和叶绿素代谢；AA.丙氨酸天冬氨酸和谷氨酸代谢；BS.次生代谢物的生物合成；MP.代谢途径；ALM.α-亚麻酸酸代谢；GS.甘氨酸、丝氨酸和苏氨酸代谢；CC.柠檬酸循环(TCA循环)；GM.谷胱甘肽代谢；NN.烟酸酯代谢；PR.蛋白酶体；OP.氧化磷酸化；GB.硫代葡萄糖苷生物合成；GG.糖酵解/糖异生；FF.黄酮和黄酮醇生物合成；ZB.玉米素生物合成；FA.脂肪酸延伸；PYM.丙酮酸代谢。SM.硒代化合物代谢；FM.果糖和甘露糖代谢；PH.吞噬体；PA.光合作用-天线蛋白；BM.丁酸代谢；PPM.丙酸酯代谢；VL.缬氨酸亮氨酸和异亮氨酸降解；AS.氨基糖和核苷酸糖代谢；CM.半胱氨酸和蛋氨酸代谢；GB.鞘糖脂生物合成-globo系列；SP.剪接体；PS.聚酮化合物糖单元生物合成；FAD.脂肪酸降解；C5.C5-支链二元酸代谢；PT.苯丙氨酸酪氨酸和色氨酸生物合成；GL.糖鞘脂生物合成；PHO.光合作用；SD.二苯乙烯类、二芳基庚烷类和姜醇生物合成；PE.过氧化物酶体；AAM.抗坏血酸和醛酸代谢；GLD.糖胺聚糖降解；TM.色氨酸代谢；PPE.内质网中的蛋白质加工；GLM.甘油脂代谢；CA.氰氨基酸代谢；OC.叶酸-碳库；GA.半乳糖代谢；CB.鞘糖脂生物合成-ganglio；MB.单萜生物合成；PP.磷酸戊糖途径。*表示显著差异(P<0.05)。
Figure 4. KEGG pathway analysis of proteins differentially expressed in two Populus allotriploid and diploid parents
PB, phenylpropanoid biosynthesis; PM, phenylalanine metabolism; GD, glyoxylate and dicarboxylate metabolism; APM, arginine and proline metabolism; NM, nitrogen metabolism; FB, flavonoid biosynthesis; LA, linoleic acid metabolism; PC, porphyrin and chlorophyll metabolism; AA, alanine aspartate and glutamate metabolism; BS, biosynthesis of secondary metabolites; MP, metabolic pathways; ALM, alpha-linolenic acid metabolism; GS, glycine, serine and threonine metabolism; CC, citrate cycle (TCA cycle); GM, glutathione metabolism; NN, nicotinate and nicotinamide metabolism; PR, proteasome; OP, oxidative phosphorylation; GB, glucosinolate biosynthesis; GG, glycolysis/gluconeogenesis; FF, flavone and flavonol biosynthesis; ZB, zeatin biosynthesis; FA, fatty acid elongation; PYM, pyruvate metabolism; SM, selenocompound metabolism; FM, fructose and mannose metabolism; PH, phagosome; PA, photosynthesis-antenna proteins; BM, butanoate metabolism; PPM, propanoate metabolism; VL, valine, leucine and isoleucine degradation; AS, amino sugar and nucleotide sugar metabolism; CM, cysteine and methionine metabolism; GB, glycosphingolipid biosynthesis-globo series; SP, spliceosome; PS, polyketide sugar unit biosynthesis; FAD, fatty acid degradation; C5, C5-branched dibasic acid metabolism; PT, phenylalanine, tyrosine and tryptophan biosynthesis; GL, glycosphingolipid biosynthesis; PHO, photosynthesis; SD, stilbenoid, diarylheptanoid and gingerol biosynthesis; PE, peroxisome; AAM, ascorbate and aldarate metabolism; GLD, glycosaminoglycan degradation; TM, tryptophan metabolism; PPE, protein processing in endoplasmic reticulum; GLM, glycerolipid metabolism; CA, cyanoamino acid metabolism; OC, one carbon pool by folate; GA, galactose metabolism; CB, clycosphingolipid biosynthesis-ganglio; MB, monoterpenoid biosynthesis; PP, pentose phosphate pathway. * represents significant difference at P<0.05 level.
表 1 两种青杨杂种三倍体子代与二倍体亲本蛋白质组差异
Table 1 Proteome differences between two Populus allotriploid and the diploid parents
组别
Group差异蛋白数
Number of DEPs占总蛋白数的百分率
Percentage in total proteins/%上调个数
Up-regulated number下调个数
Down-regulated numberFDR vs P1 43 2.9 25 18 FDR vs P2 148 10.1 60 89 SDR vs P1 29 2.0 15 14 SDR vs P2 76 3.1 27 49 注：P1代表母本，P2代表父本。下同。Notes: P1, female parent; P2, male parent. The same below. 
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