Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Towards manipulation of post-biosynthetic events in secondary metabolism of plant cell cultures

Plant cell cultures have been suggested as a feasible technology for the production of a myriad of plant-derived metabolites. However, commercial application of plant cell culture has met limited success with only a handful of metabolites produced at the pilot- and commercial-scales. To improve the production of secondary metabolites in plant cell cultures, efforts have been devoted predominantly to the optimization of biosynthetic pathways by both process and genetic engineering approaches. Given that secondary metabolism includes-the synthesis. metabolism and catabolism of endogenous compounds by the specialized proteins, this review intends to draw attention to the manipulation and optimization of post-biosynthetic events that follow the formation of core metabolite structures in biosynthetic pathways. These post-biosynthetic events-the chemical and enzymatic modifications, transport, storage/secretion and catabolism/degradation have been largely unexplored in the past. Potential areas are identified where further research is needed to answer fundamental questions that have implications for advanced bioprocess design. Anthocyanin production by plant cell cultures is used as a case study for this discussion, as it presents a good example of compounds for which there are extensive research publications but still no commercial bioprocess. It is perceived that research on post-biosynthetic processes may lead to future opportunities for significant advances in commercial plant cell cultures. (C) 2002 Elsevier Science Inc. All rights reserved.

植物细胞壁富含羟脯氨酸糖蛋白生化特性及基因克隆的研究

植物细胞壁富含羟脯氨酸糖蛋白生化特性及基因克隆的研究分成三部分： 第一部分，首先从胡萝卜愈伤组织的细胞壁中获得0.2M氯气钙可溶性蛋白质组分, 经10% TCA沉淀及羧甲基纤维素层析，分离得到一个伸展蛋白，并以SDS-聚丙烯酰胺凝胶电泳，氨基酸组成分析，分子电镜观察对所得的伸展蛋白进行了鉴定，结果表明，在胡萝卜愈伤组织中只存在一种伸展蛋白;SDS-聚丙烯酰胺凝胶电泳的考马斯蓝染色和PAS反应均为阳性，表明伸展蛋白除蛋白质组分还含有糖基;氨基酸组成分析表明，羟脯氨酸的克分子含量约占全部氨基酸的40%，丝氨酸的克分子含量约为羟脯氨酸的四分之一，含有大量的碱性和中性氨基酸，而只含有非常少量的酸性氨基酸，并且这些氨基酸克分子百分数也接近于胡萝卜富含羟脯氨酸糖蚤白基因推测出的克分子百分数。这些结果表明已经得到了一个电泳纯的伸展蛋白。伸展蛋白分子电镜观察证明它是一个棒状分子，长度为87纳米。 第二部分，用得到的伸展蛋白免疫家兔和大鼠，得到的抗体的免疫双扩散效价分别为1:2和1:1，用酶联免疫吸附分析测定的兔抗体效价为1:12，800，同时还建立了竞争性酶联免疫吸附分析测定伸展蛋白含量的标准曲线，线性范围为10-0.00001微克。利用得到的抗体对大豆下胚轴伸展蛋白的合成进行了研究。免疫荧光定位表明，大豆下胚轴表皮细胞及表皮下几层薄壁细胞有大量的荧光标记，并且这些荧光标记大部分分布在细胞质内。大豆下胚轴O.lM Tris-HCl pH7.4和0.2M氯化钙的提取物Western Blotting分析证明0.2M氯化钙提取物有与胡萝卜伸展蛋白电流性质相似的组分，并且这个组分在真菌诱导物处理的大豆下胚轴中的积累明显高于受伤处理的下胚轴。受伤和真菌诱导物处理大豆下胚轴中伸展蛋白积累的变化已经用Western Blotting分析和斑点酶联免疫吸附分析来观察，发现真菌诱导物处理的对灰斑病抗性的大豆下胚轴能够较快地积累伸展蛋白（24 - 48小时），而敏感品系的大豆下胚轴则合成伸展蛋白较晚（43-72小时）。在观察大豆下胚轴免疫荧光定位也发现类似的结果。对伸展蛋白基因的转录活性的初步研究认为抗性品系的大豆下胚轴同源mRNA转录可能早于24小时，而敏感品系大豆下胚轴同源mRNA转录可能在24小时后。以上结果认为大豆下胚轴含同源的mRNA和蛋白质组分，因此推测大豆基因组DNA有伸展蛋白基因。 第三部分，根据第二部分得到的结果，用已经得到的编码胡萝卜伸展蛋白的基因（克隆于pUC8质粒载体中）作探针，与大豆基因组DNA的EcoRI部分酶解片段杂交寻找大豆伸展蛋白基因，已经发现四个片段与探针DNA有同源性。它们的分子量分别约为23kb，8kb，5kb和2.8kb，并且23kb片段可能有更高的同源性。将23kb片段插入pUC9质粒载体上进行可隆，并用菌落原位杂交筛选获得5个克隆，对其中两个克隆用ECoRI酶解并进行分子杂交分析，重组质粒被EcoRI切成四个片段。2.8kb片段为pUC9栽体，2kb片段为与pDC5AI质粒伸展蛋白同源性较好的片段。对于23kb片段的重组质粒有待于进一步的分析。

复苏植物牛耳草Boea hygrometrica干旱诱导基因的筛选和功能分析

干旱对植物的影响和植物对干旱的反应是十分复杂的，涉及到植物的各种生理活动，由胁迫强度及时间、植物本身的遗传特性、发育阶段和生理状况以及其他环境因子共同决定。现代分子生物学和生物技术的发展深化了对植物逆境反应的研究，对植物抗旱分子反应的研究成为这个领域的热点，也引发了抗逆基因资源的争夺战。 以拟南芥等植物为实验材料的研究对深入了解植物对干旱胁迫感知和反应机制提供了重要信息, 但对植物抗旱机制的了解仍然十分匮乏。其中， 限制人们对抗旱机制深入了解的一个重要因素就是植物抗旱机制的复杂性和多样性，这种抗旱机制的复杂性决定了不是所有的机制都可通过拟南芥等植物来加以揭示。因此利用特殊生境植物来研究相关基因的表达对揭示植物对环境适应机制有着极为重要的价值。 我们实验室以复苏被子植物旋蒴苣苔（Boea hygrometrica (Bunge) R Br.，牛耳草）为实验材料，开展了多方面的工作，以期从复苏植物的角度加深人们对抗旱机制的了解。目前我们实验室已成功地建立了利用cDNA微阵列技术研究牛耳草基因表达谱的体系，并比较了4562个cDNA克隆在干旱前后的表达差异, 发现434个cDNA在干旱条件下表达水平增加一倍以上。 本工作是在上述工作的基础上，对这些表达差异的cDNA克隆并测序，利用Northern blot进一步验证这些基因。序列分析表明，这434个cDNA片段实际上代表着42个基因。根据序列同源性分析表明其中36个克隆与已知功能的基因具有同源性，它们分别是细胞壁相关基因、LEA基因和糖类、抗氧化酶类的编码基因等。另外，4个克隆未能找到同源序列，这可能意味着它们是一些新基因；2个克隆虽找到同源基因但功能未知。36个克隆中有3个编码的是细胞壁相关基因，它们在干旱早期就被诱导，而编码LEA蛋白的基因在干旱中期或后期大量诱导，这说明牛耳草耐旱反应的启动是程序化的，随干旱时间的延长和程度的加强，一步步地启动相应的基因来发挥作用，多方面地对植物细胞进行保护和修复。 本实验室的前期工作表明牛耳草脱水复水过程中细胞超微结构分发生了明显变化，其中细胞壁脱水时发生折叠复水时恢复原状。鉴于细胞壁如此显著的变化及其重要作用，我们以两个细胞壁相关的基因BhGRP1和BhGLP1为对象，对其表达的时间空间特点和对不同胁迫信号的应答、编码产物的理化性质、过量表达或抑制表达的转基因植物的表现型及转基因植物对不同逆境胁迫的抗/感性状等方面的进行研究，综合分析其在耐旱反应中可能参与的代谢途径或信号途径，以期为揭示牛耳草耐旱复苏机制提供有力的佐证。 我们利用Northern blot和半定量RT-PCR对两基因进行了表达模式分析，发现BhGRP1在干旱早期被诱导，干旱后期其转录本水平下降。而BhGLP1在早期诱导后一直保持高的表达。两者在不同胁迫、激素等处理下都有不同的响应。经PSORT分析两基因编码的蛋白都具有N-端信号肽，意味着两蛋白定位于胞外基质。构建BhGRP1-GFP和BhGLP1-GFP融合蛋白进行亚细胞定位分析，质壁分离后BhGRP1-GFP的信号仅保留在细胞壁，而BhGLP1-GFP则在胞壁胞膜上都存在。过量表达BhGRP1后发现它能赋予植物更强的耐旱复苏能力及机械强度，而抑制GLP表达的植株的抗旱性明显弱于野生型，表明BhGRP1和BhGLP1与牛耳草的耐旱复苏有密切的关系。