水稻扩展蛋白家族的生物信息学分析

扩展蛋白是植物细胞壁的重要组成部分,具有松驰细胞壁和增加细胞壁柔韧性的作用,在植物的生长发育及抗性等方面起到重要的作用。水稻的全基因组序列统计分析显示,水稻扩展蛋白基因家族包含58个成员,分属于A(34)、B(19)、LA(4)和LB(1)4个亚家族,分布在水稻10条染色体上的58个位点,且同一亚家族成员有成簇存在的现象。扩展蛋白基因长度范围为687~1128 bp,编码蛋白质具有保守的结构域,以及保守的半胱氨酸和色氨酸残基。多数情况下,亚家族成员之间的氨基酸一致率小于35%,而同一亚家族成员之间的氨基酸一致率大于35%。在内含子、外显子组成模式上,水稻扩展蛋白呈现明显的亚家族特异性,除个别基因以外,A类基因含有1或2个内含子,B类含有3个内含子,LA和LB类含有4个内含子。密码子使用统计显示,与其他物种相比,水稻中的扩展蛋白具有更多的密码子使用偏好性,有26个高频密码子存在。研究结果展示了水稻扩展蛋白基因家族的基本信息,为深入研究扩展蛋白基因的功能、探讨物种间的进化关系奠定基础。     

小立碗藓扩展蛋白基因家族的鉴定与生物信息学分析

扩展蛋白(Expansins,EXP)是一类基因家族,几乎参与了植物发育的全过程,从种子萌发到果实成熟都有扩展蛋白的参与。该研究利用生物信息学的方法对小立碗藓(Physcomitrella patens) Expansin基因家族成员进行鉴定,分析了其基因结构、染色体定位以及系统发生关系。结果表明:小立碗藓基因组中含有Expansin A(EXPA) 32个、Expansin-like A(EXLA) 6个,并未发现Expansin-like B(EXLB)及Expansin B(EXPB)。扩展蛋白氨基酸序列长度在228～290 aa之间,编码蛋白质具有两个保守的结构域Pollen_allerg_1和DPBB_1。蛋白质亚细胞定位预测结果表明:运用CELLO在线工具预测发现小立碗藓中约4/5的EXP家族基因定位于细胞外;而Euk-mPLoc预测结果则显示小立碗藓EXP基因家族成员全定位于细胞外。基因结构分析表明,小立碗藓中约68%Expansin基因有含有1～3个内含子。以上结果可为深入研究小立碗藓扩展蛋白基因的分子进化与生物学功能奠定基础。     

扩展蛋白与植物抗逆性关系研究进展

扩展蛋白是一种细胞壁蛋白,可调节细胞壁的松弛和伸展。目前研究表明,扩展蛋白几乎参与调节植物生长发育的整个进程。扩展蛋白还与植物的多种抗性反应有关,在植物对干旱、高盐以及病虫害等生物胁迫和非生物胁迫响应方面起着重要的调节作用。干旱胁迫下扩展蛋白基因的表达与植物的抗旱性有一定的关系;植物的耐盐性受到扩展蛋白基因表达的影响;淹水促进植物的伸长生长与扩展蛋白的表达密切相关;扩展蛋白调节细胞壁松弛为植物抗病性研究提供了新的思路。     

玉米扩展蛋白Expansin基因家族定位及基因表达模式分析

扩展蛋白（Expansin）是一类能够使植物细胞壁松弛的活性蛋白,在植物生长发育过程中起着重要作用。利用PLAZA、NCBI、MaizeGDB、Uniprot、PLEXdb等基因组数据库,获得玉米Expansin家族的基因序列、染色体基因座位、蛋白质序列以及长度,构建玉米Expansin基因家族系统进化树,进行基因组织表达谱的分析。结果表明,玉米基因组中含有93个Expansin基因,分布于玉米的9条染色体上;多数Expansin具有250~300个氨基酸;玉米Expansin基因家族有40个Expansin A（EXPA）、47个Expansin B（EXPB）、6个Expansin-like A（EXLA）,未发现Expansin-like B（EXLB）;44个玉米Expansin基因在不同玉米组织中特异表达。该研究结果不仅为玉米扩展蛋白的深入研究奠定了基础,而且为其他研究人员对基因信息的获取提供了参考。     

BURP蛋白家族研究进展

BURP蛋白家族是植物界中广泛存在的比较保守的结构基因家族,在胚胎形成和种子发育过程中具有功能.对BURP蛋白家族的结构特征及其4个亚家族成员的功能进行了综述.     

团花树形成层扩展蛋白基因cDNA的克隆和序列分析

以团花树(Anthocephalus chinensis)枝条形成层的cDNA为模板,参照α-Expansm基因(EXPA)序列设计兼并引物,进行RT-PCR.以得到的扩增产物为基础,采用RACE技术得到扩展蛋白基因全长cDNA,命名为AcEXPl.AcEXPl全长979 bp(GenBank注册号为FJ417847),开放阅读框为777 bp,编码258个氨基酸,并具有Expansin特有的保守序列和结构域.经过比对分析,该基因编码的氡基酸序列与毛白杨、欧洲山杨×美洲山杨、樱桃和矮牵牛的α-Expansin基因编码的氨基酸同源性分别为85%、85%、84%和83%.这为研究EXP基因与团花树木质部生长速度和材质的关系提供了基础.     

水稻与拟南芥PHD-finger蛋白的系统分析

PHD-finger(plant homeodomain finger)是具Cys4-His-Cys3特征结构的锌指蛋白结构域,它广泛存在于植物或动物转录调节蛋白中。此类蛋白在植物或动物蛋白质组中具有多个功能各异的家族成员,并在发育中扮演重要的角色。鉴定了水稻44个推定的非冗余PHD-finger蛋白,并与拟南芥蛋白质组中45个该家族成员进行了比较;所构建的2棵进化树涵盖了这89个蛋白质,暗示水稻、拟南芥与人的PHD-finger蛋白中存在共同祖先。     

中国柿果实扩展蛋白基因的cDNA克隆与序列分析

以中国柿膨大期和成熟衰老期果实cDNA为模板。参照其它植物细胞壁扩展蛋白（expansin）基因序列设计兼并引物。进行RT-PCR。得到的扩增产物与pUCm—T质粒连接。转化大肠杆菌JMl09。任意挑选阳性克隆。进行序列测定。得到2个序列不同的expansin cDNA片段。分别命名为Cdk—Exp1和Cdk—Exp2。2个片段均存在expansin基因的保守区域。即8个半胱氨酸残基和3个色氨酸残基。Cdk—Expl和Cdk—Exp2分别由531个碱基和522个碱基组成。编码177个和174个氨基酸,二者核苷酸与氨基酸序列同源性分别高达92．635％和92．156％。中国柿果实expansin cDNA与草莓、番茄和桃果实的扩展蛋白基因在氨基酸水平上有较高的同源性。     

地黄扩展蛋白基因RgExpA1的克隆与表达分析

采用RT-PCR方法对9个地黄扩展蛋白基因在地黄不同组织器官、不同发育时期的表达特点进行了分析,在此基础上用RACE方法克隆了主要在根中表达的RgExpA1基因的全长,并对该基因编码氨基酸的功能位点、拼接方式以及与同源基因的进化关系作了初步分析。     

毛竹扩展蛋白基因的鉴定及其表达分析

为全面了解毛竹中扩展蛋白的分子特征和表达模式,本研究利用生物信息学方法在毛竹基因组中共鉴定出43个扩展蛋白基因家族成员,属于4个亚家族（EXPA、EXPB、EXLA和EXLB）,分别包含18、17、7和1个成员,分布在37个Scaffold上。除PeEXPA1没有内含子和PeEXLB1含有11个内含子外,其它毛竹扩展蛋白基因的内含子为1~5个。毛竹扩展蛋白基因编码蛋白长度为91~508个氨基酸,所有的氨基酸都具有高频密码子,大部分蛋白为碱性亲水性蛋白。大部分毛竹扩展蛋白二级结构中β转角占比例最少,而β折叠占比例最大,各亚家族多数成员具有类似的三级结构。qRT-PCR结果表明,18个EXPA亚家族成员在不同组织表达存在明显差异,除PeEXPA2、PeEXPA6外其它基因表达的最高值均出现在叶片中,表明它们可能在叶片生长过程中发挥着重要作用。     

International Symposium on Insect Physiology, Biochemistry and Molecular Biology：Shandong University, Jinan, Shandong Province, China, September 19-22, 2007

We are building on the success of the Sixth Chinese Insect Physiology, Biochemistry and Molecular Biology Symposium, Beijing, held in 2005. The 2005 symposium saw many Chinese and international authorities share their expertise in a broad range of insect science, including analyses of insect genomes and proteomes, functional gene expression and regulation during development, insect immunity, insect neurobiology, insect-host interactions and insect chemical communication. The coming symposium, which will be held in Shandong University, Jinan, Shandong province, September 19-22, 2007, will offer material along similar lines.[第一段]     

Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today''s important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a “middle-out” strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from “-omics” signatures are identified as key elements of a successful systems biology modeling approach in nutrition research—one that integrates physiological mechanisms and data at multiple space and time scales.     

The Physiology, Genetics and Molecular Biology of Plant Aluminum Resistance and Toxicity

Aluminum (Al) toxicity is the primary factor limiting crop production on acidic soils (pH values of 5 or below), and because 50% of the world’s potentially arable lands are acidic, Al toxicity is a very important limitation to worldwide crop production. This review examines our current understanding of mechanisms of Al toxicity, as well as the physiological, genetic and molecular basis for Al resistance. Al resistance can be achieved by mechanisms that facilitate Al exclusion from the root apex (Al exclusion) and/or by mechanisms that confer the ability of plants to tolerate Al in the plant symplasm (Al tolerance). Compelling evidence has been presented in the literature for a resistance mechanism based on exclusion of Al due to Al-activated carboxylate release from the growing root tip. More recently, researchers have provided support for an additional Al-resistance mechanism involving internal detoxification of Al with carboxylate ligands (deprotonated organic acids) and the sequestration of the Al-carboxylate complexes in the vacuole. This is a field that is entering a phase of new discovery, as researchers are on the verge of identifying some of the genes that contribute to Al resistance in plants. The identification and characterization of Al resistance genes will not only greatly advance our understanding of Al-resistance mechanisms, but more importantly, will be the source of new molecular resources that researchers will use to develop improved crops better suited for cultivation on acid soils.     

Expansins

Biochemical dissection of the "acid-growth" process of plant cell walls led to the isolation of a new class of wall loosening proteins, called expansins. These proteins affect the rheology of growing walls by permitting the microfibril matrix network to slide, thereby enabling the wall to expand. Molecular sequence analysis suggests that expansins might have a cryptic glycosyl transferase activity, but biochemical results suggest that expansins disrupt noncovalent bonding between microfibrils and the matrix. Recent discoveries of a new expansin family and gene expression in fruit meristems and cotton fibers have enlarged our view of the developmental functions of this group of wall loosening proteins.     

丁香假单胞菌环式脂肽毒素的生理和分子生物学研究

综合评述了近10年来在丁香假单胞菌脂肽毒素生理和分子生物学研究上的发现。这些毒素依肽部AA数目可分两组。丁香假单胞霉素组(syringomycuns)已报告4个成员,肽部有9个AA;丁香假单胞肽毒素组有2个成员,肽部分别有22个和25个AA。肽部C端羧基与分子内羟基氨基酸残基(AA)的羟基酯化闭合成环,再由羟基脂肪酸酰化。两组毒素都诱导植物电解质渗漏、人和动物红血球溶解,其机制在于在细胞膜上形成二价阳离子可通过的寡体通道。对酵母菌的抑制作用受固醇的种类影响,以胆固醇的保护作用最强。丁香假单胞霉素的合成涉及一个多酶系统,有些负责肽合成,有些负责运输或调节,除受内源调节蛋白调节外,也受外源信号分子调节,尤其是受植物酚糖苷诱导。这些毒素具有抗真菌活性,对人和动物的一些病原霉菌有明显效果,在试验剂量无副作用,在医药上应用的前景良好。     

Expansins and cell growth

Expansins are now generally accepted to be key regulators of wall extension during growth. Several alternative roles for expansins have emerged in which the emphasis of their action is on wall breakdown or softening in processes such as fruit ripening, pollination, germination and abscission. Expansins are commonly encoded by substantial gene families and have classically been divided into two subfamilies, referred to as alpha- and beta-expansins. Two further subfamilies have now been identified: gamma-expansins, which were first described in Arabidopsis, and delta-expansins, which were identified in rice and are absent from Arabidopsis. Both are truncated versions of alpha- and beta-expansins, with gamma-expansins representing the amino-terminal half of a mature expansin and delta-expansins the carboxy-terminal half of a beta-expansin. Functional roles for gamma- and delta-expansins have yet to be defined, although recent data indicate a signalling role for gamma-expansins.