摘要
在过去几十年内,全球二氧化碳浓度增高的现象以及其造成的全球变暖的趋势逐渐为世界所认识并受到严重关注。从1970年到2004年,二氧化碳的排放量增加了80%(1990年到2004年增加了28%)。现在大气平均二氧化碳浓度已达到380 parts per million (ppm)。按照以往的增长速度,人们预测至本世纪末二氧化碳的浓度将上升至目前的两倍左右(IPCC 2001/2007: www.ipcc.ch)。二氧化碳浓度快速升高也促使研究者去分析植物是如何响应这种变化的从而更好地了解其对各种重要农作物的影响。在过去的二十年内,二氧化碳对植物的影响也成为了一个研究热点。其研究主要集中于对C3植物包括一些重要农作物如水稻、小麦、棉花等的生长和产量方面的研究。二氧化碳浓度的升高对植物的三大生理过程:光合作用、呼吸作用、蒸腾作用都有影响。大量研究试图通过对植物生理水平的分析来解释植物是如何响应高浓度二氧化碳的。但是由于植物响应高浓度二氧化碳是一个十分复杂的过程,其中涉及到了很多的调节蛋白、信号转导的组分和其他一些生物分子,所以从生理水平上研究得到的信息非常有限。而蛋白质是直接负责细胞功能和表型的,也是植物各种代谢过程包括对外界信号响应的执行者。因此,蛋白质组学为研究植物响应高浓度二氧化碳的机制提供了一条很好的途径。
水稻是一种单子叶的模式植物,其全基因组序列已经得到,而且有关水稻蛋白质组学的研究也比较成熟,其各个器官、组织的蛋白质组学都有报道。但是至今还没有用蛋白质组学的手段来分析植物对高浓度二氧化碳响应的研究报道。本实验是对这一领域的首次研究,主要分析了水稻幼苗对高浓度二氧化碳的快速响应(即短期影响)。
将在380ppm二氧化碳浓度(即大气环境中二氧化碳的浓度)下生长10天的水稻(Oryza sativa L. ssp Indica cv. 93-11)幼苗分别用760ppm(2x)、1140ppm(3x)、1520ppm(4x)浓度的二氧化碳连续处理各24小时,收集水稻幼苗的叶片作为处理样品,而以相应的未经处理的水稻幼苗(即在380ppm浓度二氧化碳下生长的水稻幼苗)作为对照样品。Hoagland培养液每两天更换一次。本实验使用便携式光合气体分析系统(LI6400, Li-Cor Inc, Lincoln NE, USA)分别对对照和处理的水稻进行气体交换数据测定,测定对象为从上往下数第二片叶子。主要测定的生理指标有净光合速率(Pn),气孔导度(Gs),胞间二氧化碳浓度(Ci)和蒸腾速率(E)。蛋白样品制备采用改良的TCA/Acetone方法,独立进行三次蛋白提取,然后将样品混合以减小组内误差。接下来进行二维电泳,总共6块凝胶(3个对照和3个处理样品)一起同时进行二维电泳以确保得到最大的重复性。用Blue Silver方法(改良的CBB染色方法) [191]来对蛋白质点进行染色。用UMAX PowerLook 2100XL扫描仪对凝胶进行扫描。然后用Image Master 2D Platinum software 5.0 (Amarsham Biosciences)对凝胶图像分析。每个样品选取三块重复性最好的凝胶进行分析。配比上的蛋白点都经过了手工检查。蛋白丰度用Vol%来衡量。经过统计分析,只有p-value小于0.01的蛋白点才被认为是差异蛋白。用MALDI-TOF/TOF-MS或者MS/MS鉴定差异蛋白点,得到的相关肽段信息再用MASCOT (Matrix Science)软件在NCBInr/Swiss-Prot数据库中搜索从而鉴定出这些蛋白。
生理指标的结果表明,Pn、Gs、Ci/Ca和E在1140 ppm二氧化碳浓度下达到最高,然而继续在1520 ppm下处理24小时后,则出现下降。Gs和E的变化趋势一致,因为它们都依赖于气孔的变化。总体说来,在三天的处理中对照样品的Gs在下降;对照样品在2x[CO_2]下下降了18%,在3x[CO_2]下上升了38%,而在4x [CO_2]下又下降了14.4%。相似的, E也是开始时下降了15.5%,然后又上升了28%,然后又下降了4.5%。胞间二氧化碳浓度用Ci/Ca表示(Ca:空气中CO_2浓度),在2x [CO_2]下有少许上升,在3x和4x [CO_2]下增加了20%和38%。图4.1.表示了Pn, Gs, Ci/Ca和E的变化情况。当把对照样品又放在正常二氧化碳浓度下,Pn值又会下降,即Pn是可逆的(图4.2)。
CO_2是植物光合作用的底物和碳源。碳固定是受到Rubisco的调节的。Rubisco是叶片中丰度最高的蛋白,占了可溶蛋白的50%以上。像其他的C3植物一样,二氧化碳浓度的增加会导致水稻Pn的增加,但随着对二氧化碳浓度的适应其Pn值也会逐渐降低以达到动态平衡。然而,从我们的数据可以看出Pn的迅速增加和二氧化碳浓度的增加并不是线性关系。在小麦中,当二氧化碳浓度增加到1000 ppm时,Pn和生物量显著增加,暗呼吸速率下降;而当二氧化碳浓度增加到2600ppm时,则出现相反的现象。
植物对高浓度二氧化碳的快速响应就是Pn的可逆增加。水稻叶片中Rubisco的含量从光饱和的Pn角度考虑是过量30-55%的。因此从光合作用角度来讲,只需要通过调节相关酶的活性就能响应二氧化碳浓度的增加。但是,光合作用产物的持续流出会导致其对高浓度二氧化碳的适应,这将激发一些调节机制来限制光合作用从而达到动态平衡,也就是Pn的下调。拟南芥长期处于高浓度二氧化碳(1000 ppm)下将导致非结构性碳水化合物含量增加2倍以及RbcL和RbcS表达水平显著下降(分别下降35-40%和~60% )。高浓度二氧化碳下增加的Pn会导致结构性和非结构性碳水化合物的积累,这将使细胞密度增加从而降低光的可用性,进而导致光合作用的适应。
Gs对高浓度二氧化碳的响应是多样的、可逆的、也是具有物种特异性的。总的来说,低二氧化碳浓度会导致气孔开放或者抑制气孔关闭,而高的Ci/Ca会降低气孔对高浓度二氧化碳的灵敏度,从而导致气孔的部分关闭和接下来蒸腾速率的降低。相应地,在本次试验中Pn在3x [CO_2]下达到最大值,伴随着Gs也达到最大值,但是再把[CO_2]提高到4x水平,则表现了抑制作用。而Gs和E也下降到了最低的水平(图4.1A).这可以被看成是一种适应现象。尽管还不清楚Pn的下降是否是由于Gs的下降导致的,但是从我们的数据可以看出,气孔的开闭对调节Pn是有影响的。这些生理数据也激发了我们在蛋白质水平上研究的兴趣。
对于水稻叶片蛋白质的提取我们采用的是Parker et al.,(2006)[145]报道的改良的TCA/Acetone方法,包括IEF之前进行还原和烷基化。总共发现了83个差异蛋白点,在人工检查后选取了76个蛋白点,其中57个蛋白点被PMF(55个点)和/或MS/MS(3个点)鉴定(见表.3)。正如所预料的,这些被鉴定的蛋白主要是叶绿体蛋白。其中参与光合作用的蛋白包括10个Rubisco大亚基的异构体(RbcL:11个蛋白点),Rubisco活化酶大异构体(RbcA-L)的前体(2个蛋白点), Rubisco活化酶小异构体( (RbcA-S)的前体(3个和2个蛋白点分别属于2个基因产物),putative OEPS-II (2个蛋白点)和OECP-I。这些蛋白占到了总共鉴定蛋白的34% (图4.4).还有10个参与碳代谢的蛋白点(17%)属于8个基因产物。6个参与能量通路的蛋白点属于5种蛋白,包括ATPaseβ-亚基(3个蛋白点),putative ATPase合酶,putative液泡H+-ATPase和一个putative Zn-结合的氧化还原酶(s1289)。还鉴定到了一些参与到蛋白加工、折叠和降解的分子伴侣,包括ELBP的异构体s301、s31和一个putative dnak-type分子伴侣BiP。蛋白点s323被MS/MS鉴定出两个肽段,分别属于Cucumis sativus和Chlamydonas reinnhardtii的热休克蛋白HSP-70和HSP-70B。其它蛋白包括有关信号转导(2个蛋白)、翻译、复制、氮积累、叶绿素和脂合成(各1个蛋白)等,具体分类见图2。蛋白点s1757和s1776被鉴定是APX。蛋白点s968,s1238/1300,s1004和s726通过BLASTP (www.ncbi.nlm.nih.gov/BLAST)搜索到相应的同源蛋白,通过ontology工具(www.geneontology.org)预测是与细胞定位,细胞和分子功能相关的基因,见表4。蛋白点s726与水稻中的一个预测蛋白同源,但是还没有其功能的报道。
本实验最初是希望能通过检测高浓度二氧化碳下蛋白水平的变化情况,并将其与生理水平的变化如Pn和Gs等联系起来。但是,大多数的蛋白的变化情况都不是很规律。蛋白表达量的增加和下降可能与二氧化碳浓度的增加或者某一生理水平的变化成正相关或者负相关。我们尤其关注那些显示出较大倍数水平变化的蛋白(比对照表达量高出1.5倍或者以上)。在这些蛋白中,与二氧化碳浓度正相关的蛋白有ELBP (s301),putative C2DP(s1331),putative ATP合酶(s1753)和APX (s1757) (图.4.6A)。有5个蛋白与Pn变化负相关,即随着二氧化碳浓度增加表达量下降,它们是RbcA-S (s1113),G3P的同源蛋白, dehydrogenase-A chloroplast (chl)前体(s1300)和RbcL forms (s1752, s1808, s2146)。在这些蛋白里,蛋白点s1300 and s2146表达量显著下降(图4.6B)。
还有一个奇特的趋势是一些蛋白与对照表现出相反的变化模式(图.4.6C),它们是BiP (s313),putative chaperonin 60β-前体异构体(s494, s507) , RbcA-S前体(s950 , s951) , putative glutamate-1-semialdehyde 2,1-aminomutase chl precursor (s1016) , sedoheptulose-1,7-bisphosphatase前体(s1136),G3P dehydrogenase-A chl前体同源蛋白(s1238),fructose-bisphosphate (FBP) aldolase class-I异构体(s1254, s1281),APX (s1776),RbcL forms (s2146, 1648)和ATPaseβ-亚基(s2335)。Putative chaperonin 60-β-前体异构体(s507)的变化模式与Pn类似,而ATPaseβ-亚基(s655),sedoheptulose-1,7-bisphoshate precursor (s1136)和FBP aldolase class-I (s1281)与Gs/E变化模式类似。那些在一定二氧化碳浓度下显示出最大表达量的蛋白可能对维持这一阶段的生理状态有作用。在760 ppm (2x) [CO_2]下,Pn增加了44%,而Gs和E分别下降了18%和15.5%。其中表达量增加的蛋白有putative glutamate-1-semialdehyde 2,1-aminomutase (s1016),它参与了叶绿素的生物合成。这个酶在3x [CO_2]下表达水平下降,这与对照样品的变化模式相反。其它在2x [CO_2]下表达量增加的蛋白(表达水平增加量不到1.5倍)有glutamine synthase chl前体同源蛋白(s968), minichromosome maintenance蛋白(s1463),参与到脂生物合成的putative 2-C-methyl-D-erythritol 4-phosphate cytidyl transferase (s1688)。表达量下降1.5倍或以上的蛋白有putative transketolase (s348),putative chaperonin 60β前体(s494)和ATPaseβ亚基(s2335)。其它表达量下降的蛋白(低于1.5倍)还有HSP-70 (s323), stromal 70 kDa热休克相关蛋白(s326), RbcA-L (804), RbcA-S前体(s950, s951, s1113)和RbcA-L (s819) (图4.7A)。
在1140 ppm (3x) [CO_2]下, Pn, Gs和E显示出最大值,一些蛋白包括putative液泡H+-ATPase (s405),putative phosphoglycerate mutase异构体(s437, s444),ATPaseβ-亚基(s655), putative ankyrin repeat domain protein 2同源蛋白(s1004)和RbcL (s1648)也显示出较高的表达水平,其中表达量显著增加的蛋白有putative chaperonin 60β-前体(s507)和APX (s1776)。而Rbc-L (s1543)在此处理下表达量最低。表达水平略有下降的蛋白包括RbcA-S (s959),phosphoribulokinase (PRK)前体(s1271), Rbc-L (s2087)和Rbc-L (s2146) (图4.7B)。这些蛋白表达水平的上调或者下调可能对光合速率达到最大值有作用。然而,值得注意的是尽管Pn达到最大值,而PKR表达量却略有下降。
在1520 ppm (4x) [CO_2]下, Gs/E降到最低,而且Pn也有所下降。ELBPs (s301, s310),putative dnak-type molecular chaperone BiP (s313),与一个预测蛋白同源的未知蛋白(s726),putative C2DP (s1331), putative ATP synthase (s1753)和APX (s1757)表达量显著增加。表达量显著下降的蛋白有sedoheptulose-1,7-bisphosphatase前体(s1136) ,与NADP-dependant G3P dehydrogenase chl前体同源的蛋白(s1238)。表达水平略有下降的蛋白有e FBP aldolase class-I异构体(s1281, s1254),G3P dehydrogenase同源蛋白异构体(s1300)和RbcL (s1808) (图4.7C)。
综合我们的实验结果,可以看出水稻幼苗对高浓度二氧化碳的响应首先影响了光合作用,表现为Pn的可逆增加。当处理继续进行,高光合速率使光合作用产物不断累积导致了代谢的不平衡,这将引发一些调节机制包括改变一些蛋白的表达水平使其再次达到动态平衡。蛋白质组学为我们提供了一个全面考查此过程中蛋白变化情况的平台。但是蛋白质的变化模式是非常复杂的。在本实验中有一些蛋白在对照和处理样品的表达情况正好相反(图4. 6C),它们与生理指标的变化没有明显的关联性,只能说是对高浓度二氧化碳的一种响应。Putative chaperonin 60β-precursor (s507)和Pn表现出一种正相关,而putative dnak-type molecular chaperone BiP (s313)和Pn则是一种负相关。然而,蛋白质组学分析不能表明这些蛋白水平的上调或者下调是造成生理变化的原因还是生理变化的结果。让我们意外的是, APX异构体在1140 ppm和1520 ppm高二氧化碳浓度下表达水平上调。Pn和Gs都是在1140 ppm下达到最大值,然后随着二氧化碳浓度进一步升高到1520 ppm而表现出下降,这与光合适应的现象类似。Sedoheptulose-1,7-bisphosphatase前体(s1136),与NADP-dependant G3P dehydrogenase chl前体同源的蛋白(s1238, s1300)和FBP aldolase class-I (s1254, s1281)这些参与到卡尔文循环的二磷酸核酮糖再生阶段的酶表达水平的下降也证明了光合速率的降低至少部分是由于二磷酸核酮糖的再生受到限制造成的。有一个预测的线粒体ATPase在高二氧化碳浓度下表达水平上调,这也暗示暗呼吸速率可能也在增加。虽然本实验没有鉴定到一些以前已经研究过对高浓度二氧化碳响应的酶如己糖激酶,蔗糖磷酸合酶,琥珀酸脱氢酶和细胞色素C氧化酶等。但是,本实验首次研究了水稻幼苗对高浓度二氧化碳的短期响应。关于水稻叶片对长期二氧化碳浓度的响应以及更广pIs范围内研究蛋白表达水平的变化情况将为这一领域提供更多有用的信息。
质外体,细胞质膜体以外的所有空间,包括细胞壁、细胞间隙及分化成熟的木质部,这些是与调节、信号转导和防御相关的一些重要蛋白的场所。尽管有一些关于植物各个组织或器官的质外体蛋白质组的提取和鉴定的报道,但是水稻质外体蛋白质组目前研究的还不多。目前为止,仅报道鉴定到了9个水稻叶片质外体蛋白[10]。所以对于水稻叶片和根部质外体蛋白的研究将利于我们更好理解水稻信号转导和防御机制。我们希望能够改良真空渗透-离心法来提取质外体蛋白,为今后研究各种生物或者非生物胁迫包括高浓度二氧化碳响应的质外体蛋白质组研究提供一个平台。
质外体蛋白可以分为两大类:1)可溶性蛋白或者与细胞外基质连接松散的蛋白,2)部分或者全部嵌入到细胞壁的蛋白,包括一些伸出到细胞外基质的跨膜蛋白。
通常来讲,提取质外体蛋白有两种方法:
i)破裂法:研磨植物器官或者组织,匀浆化后用亚细胞分离的方法提纯细胞壁,然后再用不同的萃取液将蛋白提取出来。
ii)非破裂法:最常使用的方法是真空渗透-离心法(VIC)[170]。可溶性蛋白或者与细胞壁结合松散的蛋白可用适当的提取缓冲液提取,而不破坏细胞膜的完整性。
这两种方法各有利弊。破裂法可以提取到与细胞壁紧密结合的蛋白,但是由于组分分离不纯和细胞破裂等原因使其很容易受到细胞质蛋白的污染。而真空渗透-离心法对于提取与细胞壁结合松散的蛋白是最适合的,但是要保证细胞膜的完整性,而且其提取效率非常低。因此要提取足够蛋白质组学分析用的质外体蛋白且不受细胞质蛋白的污染是技术上的一大挑战。因此我们需要对提取方法进行优化,以满足这两方面的需要。
为了解决提取产率低的问题,我们自制了一种容器(图3.1 ) ,它能使每个管子装入10g新鲜水稻的根和4g的叶片。每次使用4个管子(~ 40 g根和16 g叶片),然后提取3-4次(每次重复两遍),可得到足够进行3-5次24cm胶条的二维电泳(银染)的蛋白。用Buffer B提取时,平均每次大概能得到1.2 ml和800μl的水稻根部和叶片的提取液(表.5)。在1000xg,离心10分钟的条件下能收集到最多的提取液并且污染最小,这也与以前的报道相符[170, 223]。将3-4次的根部和叶片提取液分别混合起来然后浓缩50-80和20倍,最终达到500-600μl。然后进行G6PDH酶活检测[190]来判断污染情况并用Bradford法测定蛋白浓度。然后将提取液用等体积的20%TCA/Acetone沉淀来提取蛋白。
二维电泳凝胶上蛋白点的数目和分布主要取决于提取缓冲液的使用。Tris-HCl是一种最常使用的溶解和提取复杂蛋白混合样品的缓冲液。像KCl和NaCl这些盐也经常被用来帮助提取一些结合蛋白。在A. thaliana rosette [180]里,CaCl2 (0.2 M)被证明能提取到最多的质外体蛋白,但是也有报道指出CaCl2会对细胞膜造成损伤。EDTA,EGTA和CDTA是经常使用的螯合剂可以帮助提取一些与胶质结合的蛋白[224]。硼酸盐缓冲液可用来提取一些与细胞壁通过糖苷键结合的蛋白。甘露醇或者山梨醇被用作渗透剂在提取过程中保护细胞膜不受损伤。以0.05 M Tris-HCl pH 7.6 (或者没有Tris)缓冲液为基础,用各种不同盐的组合,还有加入或者不加入非离子的变性剂,Triton X-100(利于疏水蛋白提取)等多种提取液进行试验,见第三章。
针对缓冲液B, G和H我们进行了定量二维电泳(图5.1)。与设想的不同,缓冲液G的结果并不理想。凝胶酸性区域(左上方)的蛋白点并不清晰,尽管已经通过不断浓缩除盐。缓冲液B显示出最多的蛋白点数,尤其是在酸性区域,而且质量也比较好。缓冲液H看起来和缓冲液B的效果差不多,而且在pI 6-9的上方区域可观察到更多的蛋白点(图5.1)。
表..为我们列举了缓冲液B的最大提取效率。其平均的提取效率为:根的质外体蛋白大概是15μg/g FW ,叶片大概是30μg/g FW (表7)。VIC方法本身的提取效率就十分低,加上我们用的是新鲜湿重的样品来计算,所以效率较低。G6PDH酶活试验表明根部的污染小于1% ,而在叶片提取液中没有发现污染(表7)。
基于较高的提取效率(与其它缓冲液相比),较低的污染水平和高质量的凝胶图谱,我们认为缓冲液B是提取水稻叶片和根部质外体蛋白的最佳提取缓冲液。图5.2和图5.3为我们显示了根部和叶片质外体蛋白与总蛋白的凝胶图谱。通过比对不难看出,我们确实富积到了一些质外体蛋白。在pI 3-10的凝胶上,我们分别发现了根部和叶片超过400个和大概150个蛋白点。另外,在pI 3-10的凝胶上我们发现了一些水平条纹。因此我们用了DeStreak试剂,虽然它能够提高碱性区域的溶解性,但是在此区域没有很多蛋白点。(图5.2.A)。由于蛋白点主要集中在pI 4-7的范围内,所以我们最终选用了pI 4-7的胶条,结果得到了高质量重复性较好的凝胶图谱(图5.3.A),这为我们今后分析不同处理下质外体差异蛋白的研究奠定了基础。
Previous investigations of plants’response to elevated CO_2 were mostly based on physiological measurements and biochemical assays. In this study proteomic approach was employed to investigate plants response to higher CO_2 levels using rice as a model. Ten days old seedlings were progressively exposed to 760 ppm, 1140 ppm and 1520 ppm CO_2 concentrations for 24 h each. Net photosynthesis rate (Pn), stomatal conductance (Gs), transpiration rate (E) and intracellular to ambient CO_2 concentration ratio (Ci/Ca) were measured. Pn, Gs and E showed maximum increase at 1140 ppm CO_2 but further exposure to 1520 ppm for 24h resulted in down regulation of these. Proteins extracted from leaves were subjected to 2-DE analysis and 57 spots showing differential expression patterns, as detected by profile analysis, were identified by MALDI-TOF/TOF-MS. Most of the proteins belonged to photosynthesis, carbon-metabolism and energy pathways. Several molecular chaperones and ascorbate peroxidase were also found responding to higher CO_2 levels. Correlations between the protein expression patterns and the photosynthetic measurements at the three CO_2 levels were explored. Concomitant with the down regulation of Pn and Gs, the levels of enzymes of the regeneration phase of the Calvin cycle were decreased. Apoplast, the extracellular matrix, is a seat of important signaling and stress/defense related proteins. Rice apoplast proteins are largely unexplored. In a subsidiary study, apoplast extraction method was optimized using vacuum infiltration-centrifugation technique. More than 400 and 150 protein spots were visualized in pI 3-10 range from roots and leaves extracts. 2-D gels in pI 4-7 range showed high quality and reproducibility. Further improvements in the method for differential protein analysis are suggested.
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