Localization of an Arg-Gly-Asp recognition site within an integrin adhesion receptor

Many adhesive interactions are mediated by Arg-Gly-Asp (RGD) sequences within adhesive proteins. Such RGD sequences are frequently recognized by structurally related heterodimers that are members of the integrin family of adhesion receptors. A region was found in the platelet RGD receptor, gpIIb/IIIa, to which an RGD peptide becomes chemically cross-linked. This region corresponds to residues 109 to 171 of gpIIIa. This segment is conserved among the beta subunits of the integrins (76 percent identity of sequence), indicating that it may play a role in the adhesive functions of this family of receptors.     

茶树ZF-HD转录因子基因家族的鉴定及表达分析

【目的】搜索鉴定茶树ZF-HD（Zinc finger homeodomain）转录因子基因家族成员,并对其进行生物信息学分析及在不同组织及非生物胁迫和激素处理下的表达模式,为茶树ZF-HD基因家族的功能研究及茶树遗传性状改良提供理论依据。【方法】通过隐马尔可夫模型预测和序列比对从茶树基因组中筛选鉴定出茶树ZF-HD基因家族成员,利用在线生物信息学分析软件对其基因结构、启动子元件,以及编码蛋白的理化性质、氨基酸序列、结构特征、进化关系等进行预测分析,并基于转录组测序（RNA-Seq）数据分析其在不同组织及在干旱胁迫、盐胁迫和茉莉酸甲酯（MeJA）处理下的表达模式。【结果】从茶树基因组中鉴定出17个ZF-HD基因家族成员（CsZHD1~CsZHD17）,其编码区（CDS）序列长度为369~2187 bp,编码122~728个氨基酸残基,蛋白分子量13.51~80.42 kD,理论等电点为6.09~9.19,均属于亲水性不稳定蛋白,蛋白二级结构均由β-转角、延伸链、α-螺旋和无规则卷曲构成。除CsZHD2、CsZHD5和CsZHD7蛋白定位于细胞质,CsZHD9蛋白定位于细胞外,其他13个蛋白均定位于细胞核。仅CsZHD2、CsZHD7、CsZHD9、CsZHD10和CsZHD12基因含外显子和内含子,其他12个CsZHDs基因均无内含子。除CsZHD7蛋白具有2个ZF-HD_dimer结构域外,其他16个蛋白均具有1个ZF-HD_dimer结构域。CsZHD1~CsZHD17蛋白具有2~5个保守基序（motif）,其中motif 1和motif 3为共有的保守基序。茶树ZF-HD家族蛋白可分为5个亚族（ZHDⅠ、ZHDⅡ、ZHDⅢ、ZHDⅣ和MIF）,较拟南芥少了ZHDⅤ亚族。除CsZHD2、CsZHD12和CsZHD17基因在8个组织中不表达或表达量极低外,其他14个CsZHDs基因在8个组织中呈差异性表达;除CsZHD2、CsZHD12和CsZHD17基因外,其他15个CsZHDs基因在顶芽或花中表达量较高。在干旱胁迫和盐胁迫处理下,除CsZHD1、CsZHD2、CsZHD5、CsZHD12、CsZHD14和CsZHD17基因的表达量始终处于较低水平外,其他CsZHDs基因均呈不同的变化趋势;在MeJA处理下,除CsZHD2、CsZHD5和CsZHD12基因表达量极低外,多数CsZHDs基因呈下调表达的趋势。【结论】从茶树基因组中鉴定出17个ZH-HD基因家族成员,其编码蛋白具有保守的锌指结构域和同源异型盒结构域;茶树与拟南芥ZH-HD基因家族相比缺少ZHDⅤ亚族;CsZHDs基因的表达具有组织特异性,且大多数成员的表达受非生物胁迫和MeJA的影响。     

An alternative bactericidal mechanism of action for lantibiotic peptides that target lipid II

Lantibiotics are polycyclic peptides containing unusual amino acids, which have binding specificity for bacterial cells, targeting the bacterial cell wall component lipid II to form pores and thereby lyse the cells. Yet several members of these lipid II-targeted lantibiotics are too short to be able to span the lipid bilayer and cannot form pores, but somehow they maintain their antibacterial efficacy. We describe an alternative mechanism by which members of the lantibiotic family kill Gram-positive bacteria by removing lipid II from the cell division site (or septum) and thus block cell wall synthesis.     

水稻半纤维素支链合酶基因GT61家族的结构特征和组织表达分析

从生物信息学和基因表达的角度,鉴定OsGT61家族成员的结构特征和组织表达特性。结果表明,OsGT61家族含有25个成员,分为3个亚类。A、B和C亚类分别含有19、3和3个成员,其基因的外显子数介于1~7个。其蛋白质大小为49.1~73.8ku,pI为5.4~10.4。该家族蛋白质的C端motif较为保守。而且,它们含有Ser/Thr激酶的磷酸化位点分别为9~29个和3~13个,Tyr激酶的磷酸化位点小于7个。但是,该家族成员的糖基化位点相对较少,16个成员存在1~4个O-糖基化位点,3个蛋白存在1~2个N-糖基化位点。基因表达芯片聚类分析和半定量RT-PCR检测表明,OsGT61基因家族主要成员在不同组织中表达水平存在明显差异。这些结果暗示OsGT61家族基因在水稻不同组织中细胞壁半纤维素生物合成中发挥不同作用。     

Disruption of signaling by Yersinia effector YopJ, a ubiquitin-like protein protease

Homologs of the Yersinia virulence effector YopJ are found in both plant and animal bacterial pathogens, as well as plant symbionts. These YopJ family members were shown to act as cysteine proteases. The catalytic triad of the protease was required for inhibition of the mitogen-activated protein kinase (MAPK) and nuclear factor kappaB (NF-kappaB) signaling in animal cells and for induction of localized cell death in plants. The substrates for YopJ were shown to be highly conserved ubiquitin-like molecules, which are covalently added to numerous regulatory proteins. YopJ family members exert their pathogenic effect on cells by disrupting this posttranslational modification.     

谷子MRP蛋白家族序列特征、分子进化及表达模式分析

本研究旨在深入了解谷子叶酸转运家族成员的基因结构和表达模式,为谷子体内叶酸转运分子机制的研究奠定基础。使用Phytozome、Clustal X、MEGA7.0等在线工具和软件,对谷子MRP家族成员进行生物信息学分析;基于谷子谷穗有参转录组测序数据,分析谷子MRP家族成员表达模式。结果显示,谷子MRP蛋白家族成员共21个,在7号染色体分布最多,有8个基因;17个谷子MRP蛋白偏碱性和4个偏酸性,根据疏水值判断其均为亲水性蛋白;成员SiMRP7、SiMRP12基因的表达量与谷子组织中的总叶酸含量表现出协同降低的趋势,推测这两个蛋白可能对谷子叶酸的积累起到调控作用。本研究有助于进一步鉴定叶酸转运相关蛋白,为后续研究叶酸代谢途径及谷子基因挖掘提供了理论基础。     

Sequence of the envelope glycoprotein gene of type II human T lymphotropic virus

The sequence of the envelope glycoprotein gene of type II human T lymphotropic virus (HTLV) is presented. The predicted amino acid sequence is similar to that of the corresponding protein of HTLV type I, in that the proteins share the same amino acids at 336 of 488 residues, and 68 of the 152 differences are of a conservative nature. The overall structural similarity of these proteins provides an explanation for the antigenic cross-reactivity observed among diverse members of the HTLV retrovirus family by procedures that assay for the viral envelope glycoprotein, for example, membrane immunofluorescence.     

拟南芥PGK基因家族功能的初步分析

磷酸甘油酸激酶(Phosphoglycerate kinase)是一类进化上非常保守的蛋白家族,因而利用模式植物拟南芥研究PGK家族基因功能具有普遍意义。拟南芥基因组中含有三个PGK基因家族成员(PGK1,PGK2和PGK3),但是对于它们的基因表达模式和蛋白定位的研究还不是很清楚。本文利用实时荧光定量PCR技术检测了PGK基因家族的表达模式,结果表明三个PGK基因在拟南芥的各个组织器官和发育阶段中都有表达。利用拟南芥原生质体瞬时转化系统对三个PGK蛋白进行亚细胞定位,结果显示PGK1和PGK3定位于细胞基质,而PGK2定位于叶绿体。另外,我们分离得到了PGK2基因的T-DNA插入敲除突变体pgk2。pgk2在正常条件下表现出叶片黄化,PR1基因上调表达和H_2O_2过量积累等类似于超敏反应的细胞死亡表型。进一步的遗传分析表明pgk2的细胞死亡表型和T-DNA插入位点紧密连锁,暗示着pgk2的细胞死亡表型是由于PGK2的基因缺失造成的,因此PGK2可能在调控植物细胞程序化死亡过程中有重要作用。以上研究结果对于进一步探讨PGK基因家族的功能具有重要的参考价值。     

Genome-wide Analysis of Ovate Family Proteins in Arabidopsis

Arabidopsis thaliana ovate family proteins (AtOFPs) is a newly found plant-specific protein family interacting with TALE (3-aa loop extension homeodomain proteins) homeodomain proteins in Arabidopsis. ...     

Dodeca-CLE peptides as suppressors of plant stem cell differentiation

In plants and animals, small peptide ligands that signal in cell-cell communication have been suggested to be a crucial component of development. A bioassay of single-cell transdifferentation demonstrates that a dodecapeptide with two hydroxyproline residues is the functional product of genes from the CLE family, which includes CLAVATA3 in Arabidopsis. The dodecapeptide suppresses xylem cell development at a concentration of 10(-11) M and promotes cell division. An application, corresponding to all 26 Arabidopsis CLE protein family members, of synthetic dodecapeptides reveals two counteracting signaling pathways involved in stem cell fate.     

稻瘟病菌假定的糖基水解酶62家族初步研究

 【目的】了解糖基水解酶62家族细胞壁降解酶系在稻瘟病菌致病中的作用。【方法】通过生物信息学方法对稻瘟病菌基因组中假定的糖基水解酶62家族成员进行基因结构、蛋白分泌特性及系统发育分析,并对其中一个成员MGG_01403.6进行过量表达、基因敲除分析。【结果】该家族共有8个成员,均具有细胞壁降解酶（糖基水解酶62家族）保守结构域,且均为胞外分泌蛋白;系统发育分析可以将这些成员分别聚类在两个进化分支中;成员间在不同侵染阶段表达模式有差异;MGG_01403.6过量表达和基因敲除均不影响稻瘟病菌的致病性。【结论】糖基水解酶62家族可能存在功能冗余作用,进一步的双突变或多突变可能是明确这类多基因家族基因功能的重要方法。     

番茄CKX基因家族生物信息学分析

植物细胞内的细胞分裂素受到细胞分裂素脱氢酶/氧化酶(Cytokinin oxidase/dehydrogenase,CKX)的调节,来维持植物体内细胞分裂素动态平衡。为探究番茄基因组中CKX基因(SlCKX)家族成员的信息,本研究通过现代生物信息学分析,对番茄中CKX基因家族进行鉴定和分析。结果表明,在番茄全基因组中鉴定出9个CKX基因家族成员,蛋白长度在453~553氨基酸之间,编码蛋白分子量在51660.72~52493.64kDa之间,为亲水性蛋白;番茄CKX基因分在4个亚族内,并且SlCKX家族成员中含有3~5的内含子以及4~6外显子;9个番茄CKX家族基因不均匀的分布在5条染色体上,番茄CKX基因家族包含11种顺式作用元件,其中分布最广的为脱落酸响应元件。该研究将为番茄CKX基因家族的功能和应用研究提供一定的理论依据。     

植物锌铁转运蛋白 ZIP 家族的生物信息学分析

锌铁转运蛋白ZIP家族成员对于控制植物体内锌铁平衡具有非常重要的作用.采用生物信息的方法对植物锌铁转运蛋白序列结构、性质及分子进化进行分析预测,结果发现,该蛋白由226～459个氨基酸组成,是一个多次跨膜蛋白,多数成员定位于细胞质膜、叶绿体膜及液泡膜上,其分子进化历程与物种进化历程并不一致,提示该蛋白序列分歧时间较早.研究结果能够为该蛋白基因的克隆、结构和功能的进一步深入研究提供理论基础.     

Functional polymorphism among members of abscisic acid receptor family(ZmPYL) in maize

Pyrabactin resistance 1-like proteins(PYLs) are direct receptors of abscisic acid(ABA). For the redundant and polymorphic functions, some members of the PYL family interact with components of other signaling pathways. Here, 253 positive colonies from a maize cDNA library were screened as interacting proteins with the members of ZmPYL family. After sequencing and function annotation, 17 of 28 interaction combinations were verified by yeast two-hybrid(Y2 H). The germination potential, taproot length and proline content of a quartet mutant of Arabidopsis PYL genes were significantly deceased comparing to the wild type(WT) under alkaline stress(pH 8.5) and 100 μmol L–1 methyl jasmonate(MeJA) induction. The malondialdehyde(MDA) content was significantly increased. After germinating in darkness, the characteristics of dark morphogenesis of the quartet mutant seedlings were more obvious than those of the WT. The differential expression of the related genes of photomorphogenesis in the mutant was much more than that in the WT. Three light and two JA responsive cis-affecting elements were identified during the promoter sequences of the AtPYL1 and AtPYL2 genes. These results suggested that functional polymorphism has evolved among the members of ZmPYL family. In response to developmental and environmental stimuli, they not only function as direct ABA receptors but also interact with components of other signaling pathways mediated JA, brassinosteroid(BR), auxin, etc., and even directly regulate downstream stress-related proteins. These signaling pathways can interact at various crosstalk points and different levels of gene expression within a sophisticated network.     

Antibody active sites and immunoglobulin molecules

In order to obtain detailed information about the relationship between structure and function in antibody molecules, a method called affinity labeling has been devised to attach chemical labels specifically to amino acid residues in the active sites of antibody molecules. With antibodies to three different haptens, highly specific labeling of the active sites has been achieved. Tyrosine residues on both heavy and light polypeptide chains have been labeled in a molar ratio close to 2:1, and labels on the two chains are equally specific to the active sites. Peptide fragmentation studies of the labeled chains of one antibody system have shown that: (i) within 25 amino acid residues of the labeled tyrosine on either chain, substantial chemical heterogeneity exists among different antibody molecules of the same specificity; and (ii) the labeled peptide fragments from both chains are very similar in physicochemical characteristics, including average size, heterogeneity, and unusual hydrophobicity. These experimental results have led us to the view that a particular region of the heavy chain and a particular region of the light chain are utilized to construct the active sites of the three different antibodies, differences in specificity arising from chemical perturbations in these two regions. Correlated structural studies of affinity-labeled antibodies and of the homogeneous light chains (Bence Jones proteins) and heavy chains produced in multiple myeloma may permit the identification of these special active-site regions. The view that active sites of different specificity are chemical perturbations of a particular region of the antibody molecule has a possible close analogue in enzyme systems, particularly among the esterases. The marked chemical similarities we have observed between the active site regions of heavy and light chains indicate to us that chemical homologies, but not identities, exist between the chains. This is reinforced by recently obtained amino acid sequence data which reveal homologies between the two chains near their carboxyl-terminals. These results indicate that the structural genes which code for the synthesis of heavy and light chains are related, presumably having arisen from some common ancestral gene during evolution. This conclusion strongly suggests that both heavy and light chains determine antibody specificity, and has important implications for the still-unknow mechanisms of antibody biosynthesis.     

Identification and functional expression of the mitochondrial pyruvate carrier

The transport of pyruvate, the end product of glycolysis, into mitochondria is an essential process that provides the organelle with a major oxidative fuel. Although the existence of a specific mitochondrial pyruvate carrier (MPC) has been anticipated, its molecular identity remained unknown. We report that MPC is a heterocomplex formed by two members of a family of previously uncharacterized membrane proteins that are conserved from yeast to mammals. Members of the MPC family were found in the inner mitochondrial membrane, and yeast mutants lacking MPC proteins showed severe defects in mitochondrial pyruvate uptake. Coexpression of mouse MPC1 and MPC2 in Lactococcus lactis promoted transport of pyruvate across the membrane. These observations firmly establish these proteins as essential components of the MPC.     

大白菜GIF蛋白家族的生物信息学分析

GIF(GRF-interacting factor)家族是一类含有SNH和QG结构域的蛋白质,可与GRF(Growth reg-ulating factor)转录因子蛋白相结合形成功能复合体,通过促进和维持细胞的分裂能力参与调控植物叶器官的发育。本研究系统鉴定了5个大白菜的GIF基因,并对这些基因编码的蛋白质序列进行了保守性和系统进化分析,最后对BrGIF1基因的表达进行了分析。结果表明,所有的大白菜和拟南芥GIF蛋白家族成员都具有高度保守的SNH和QG结构域。在进化上,GIF蛋白家族可分为两个不同的亚家族,并且这种特征在大白菜和拟南芥分离之前就已经形成。在表达模式上,BrGIF1基因在具有较大叶球的白菜自交系以及具有较强细胞分裂能力的组织中的转录表达水平较高。另外,BrGIF1基因的表达受到NAA的诱导和ABA的抑制。这些结果表明大白菜GIF蛋白可能具有和拟南芥GIF蛋白相似的生物学功能,在调控植物器官发育中具有重要作用。     

Reduced MAP kinase phosphatase-1 degradation after p42/p44MAPK-dependent phosphorylation

The mitogen-activated protein (MAP) kinase cascade is inactivated at the level of MAP kinase by members of the MAP kinase phosphatase (MKP) family, including MKP-1. MKP-1 was a labile protein in CCL39 hamster fibroblasts; its degradation was attenuated by inhibitors of the ubiquitin-directed proteasome complex. MKP-1 was a target in vivo and in vitro for p42(MAPK) or p44(MAPK), which phosphorylates MKP-1 on two carboxyl-terminal serine residues, Serine 359 and Serine 364. This phosphorylation did not modify MKP-1's intrinsic ability to dephosphorylate p44(MAPK) but led to stabilization of the protein. These results illustrate the importance of regulated protein degradation in the control of mitogenic signaling.