Bioinformatic identification of genes encoding C1q-domain-containing proteins in zebrafish

C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immunities. The globular (gC1q) domain similar with C1q was also found in many non-complement C1q-domain-containing (C1qDC) proteins which have similar crystal structure to that of the multifunctional tumor necrosis factor (TNF) ligand family, and also have diverse functions. In this study, we identified a total of 52 independent gene sequences encoding C1q-domain-containing proteins through comprehensive searches of zebrafish genome, cDNA and EST databases. In comparison to 31 orthologous genes in human and different numbers in other species, a significant selective pressure was suggested during vertebrate evolution. Domain organization of C1q-domain-containing (C1qDC) proteins mainly includes a leading signal peptide, a collagen-like region of variable length, and a C-terminal C1q domain. There are 11 highly conserved residues within the C1q domain, among which 2 are invariant within the zebrafish gene set. A more extensive database searches also revealed homologous C1qDC proteins in other vertebrates, invertebrates and even bacterium, but no homologous sequences for encoding C1qDC proteins were found in many species that have a more recent evolutionary history with zebrafish. Therefore, further studies on C1q-domain-containing genes among different species will help us understand evolutionary mechanism of innate and acquired immunities.

Zebraflsh z-otu, a novel Otu and Tudor domain-containing gene, is expressed in early stages of oogenesis and embryogenesis

Several studies have suggested that Otu domain had de-ubiquitinating activity and Tudor domain was important for the formation of germ cells. Here, we reported a novel zebrafish ovary-specific gene containing Otu and Tudor domain, z-otu, which was expressed at stages I-III oocytes and embryonic stages from zygotes to early blastula during embryonic cells maintained their totipotency. Therefore, z-otu might link the ubiquitin signaling pathway to early oogenesis and maintaining the totipotency of embryonic cell. (c) 2005 Elsevier B.V. All rights reserved.

A novel C1q-domain-containing protein from Zhikong scallop Chlamys farreri with lipopolysaccharide binding activity

The C1q-domain-containing (C1qDC) proteins are a family of proteins characterized by a globular C1q (gC1q) domain in their C-terminus. They are involved in various processes of vertebrates and supposed to be an important pattern recognition receptor in innate immunity of invertebrates. In this study, a novel member of C1q-domain-containing protein family was identified from Zhikong scallop Chlamys farreri (designated as CfC1qDC) by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of CfC1qDC was of 777 bp, consisting of a T-terminal untranslated region (UTR) of 62 bp and a 3' UTR of 178 bp with a polyadenylation signal sequence AATAAA and a poly (A) tail. The CfC1qDC cDNA encoded a polypeptide of 178 amino acids, including a signal peptide and a C1q-domain of 158 amino acids with the theoretical isoelectric point of 5.19 and the predicted molecular weight of 17.2 kDa. The C1q-domain in CfC1qDC exhibited homology with those in sialic acid binding lectin from mollusks and C1qDC proteins from higher vertebrates. The typical 10 beta-strand jelly-roll folding topology structure of C1q-domain and the residues essential for effective packing of the hydrophobic core were well conserved in CfC1qDC. By fluorescent quantitative real-time PCR, mRNA transcripts of CfC1qDC were mainly detected in kidney, mantle, adductor muscle and gill, and also marginally detectable in hemocytes. In the bacterial challenge experiment, after the scallops were challenged by Listonella anguillarum, there was a significant up-regulation in the relative expression level of CfC1qDC and at 6 h post-injection, the mRNA expression reached the maximum level and was 4.55-fold higher than that of control scallops. Similarly, the expression of CfC1qDC mRNA in mixed primary cultures of hemocytes stimulated by lipopolysaccharides (LPS) was up-regulated and reached the maximum level at 6 h post-stimulation, and then dropped back to the original level gradually. In order to investigate its function, the cDNA fragment encoding the mature peptide of CfC1qDC was recombined and expressed in Escherichia coli BL21 (DE3). The recombinant CfC1qDC protein displayed a significantly strong activity to bind LIDS from E. coli, although no obvious antibacterial or agglutinating activity toward Gram-negative bacteria E. coli JM109, L. anguillarum and Gram-positive bacteria Micrococcus luteus was observed. These results suggested that CfC1qDC was absolutely a novel member of the C1qDC protein family and was involved in the recognition of invading microorganisms probably as a pattern recognition molecule in mollusk. (c) 2008 Elsevier Ltd. All rights reserved.

AiC1qDC-1, a novel gC1q-domain-containing protein from bay scallop Argopecten irradians with fungi agglutinating activity

The globular C1q-domain-containing (C1qDC) proteins are a family of versatile pattern recognition receptors via their globular C1q (gC1q) domain to bind various ligands including several PAMPs on pathogens. In this study, a new gC1q-domain-containing protein (AiC1qDC-1) gene was cloned from Argopecten irradians by rapid amplification of cDNA ends (RACE) approaches and expressed sequence tag (EST) analysis. The full-length cDNA of AiC1qDC-1 was composed of 733 bp, encoding a signal peptide of 19 residues and a typical gC1q domain of 137 residues containing all eight invariant amino acids in human C1qDC proteins and seven aromatic residues essential for effective packing of the hydrophobic core of AiC1qDC-1. The gC1q domain of AiC1qDC-1, which possessed the typical 10-stranded beta-sandwich fold with a jelly-roll topology common to all C1q family members, showed high homology not only to those of Cl qDC proteins in mollusk but also to those of C1qDC proteins in human. The AiC1qDC-1 transcripts were mainly detected in the tissue of hepatopancreas and also marginally detectable in adductor, heart, mantle, gill and hemocytes by fluorescent quantitative real-time PCR. In the microbial challenge experiment, there was a significant up-regulation in the relative expression level of AiC1qDC-1 in hepatopancreas and hemocytes of the scallops challenged by fungi Pichia pastoris GS115, Gram-positive bacteria Micrococcus luteus and Gram-negative bacteria Listonella anguillarum. The recombinant AiC1qDC-1 (rAiC1qDC-1) protein displayed no obvious agglutination against M. luteus and L. anguillarum, but it aggregated P. pastoris remarkably. This agglutination could be inhibited by D-mannose and PGN but not by LPS, glucan or D-galactose. These results indicated that AiC1qDC-1 functioned as a pattern recognition receptor in the immune defense of scallops against pathogens and provided clues for illuminating the evolution of the complement classical pathway. (C) 2010 Elsevier Ltd. All rights reserved.

Identification, expression, function and localization of a DUF985 domain-containing hypothetical gene from amphioxus Branchiostoma belcheri

The progress in genome sequencing has led to an increasing submission of uncharacterized hypothetical genes with the domain of unknown function, DUF985, in GenBank, and none of these genes is related to a known protein. We therefore underwent an experimental study to identify the function of a DUF985 domain-containing hypothetical gene BbDUF985 (GenBank Accession No. AY273818) isolated from amphioxus Branchiostoma belcheri (B. belcheri). BbDUF985 was successfully expressed in both prokaryotic and eukaryotic systems, and its recombinant proteins expressed in both systems definitely exhibited an activity of phosphoglucose isomerase (PGI). Both tissue-section in situ hybridization and immunohistochemistry demonstrated that BbDUF985 was expressed in a tissue-specific manner, with most abundant levels in the hepatic caecum and ovary. In CHO cells transfected with the expression plasmid pEGFP-N1/BbDUF985, the fusion protein was targeted in the cytoplasm of CHO cells, suggesting that BbDUF985 is a cytosolic protein. In contrast, Western blotting indicated that BbDUF985 was also present in amphioxus humoral fluids, suggesting that it exists as a secreted protein as well. Our study provided a framework for further understanding the biochemical properties and physiological function of DUF985-containing hypothetical proteins in other species. (c) 2008 Elsevier Inc. All rights reserved.

SmC2P1, a C2 domain protein from Scophthalmus maximus that binds bacterial pathogen-infected lymphocytes and reduces bacterial survival

C2 domains are protein structural modules found in many eukaryotic proteins involved in signal transduction, membrane trafficking, and immune defense. Most of the studied C2 domain-containing proteins are multi-domained in structure, in which the C2 domain is an independently folded motif and plays an essential role in calcium-dependent membrane-targeting. Although C2 domains isolated from intact proteins have been studied for biological functions, no study on natural proteins containing C2 domain only has been documented. In this study, we identified a Scophthalmus maximus protein SmC2P1 that is comprised of a single C2 domain and lacks any other apparent domain structures. The deduced amino acid sequence of SmC2P1 contains 129 residues and shares 36-38% identities with the C2 domains of the perforins of several fish species. Like typical C2 domains, SmC2P1 is predicted to organize into eight beta-strands with a Ca2+-binding site located in inter-strand loops. SmC2P1 expression was detected, in deceasing order, in liver, spleen, blood, brain, muscle, kidney, gill, and heart. Experimental challenge of turbot with a bacterial pathogen significantly upregulated SmC2P1 expression in kidney in a time-dependent manner. Recombinant SmC2P1 purified from yeast exhibits no hemolytic activity but binds to pathogen-infected kidney lymphocytes in the presence of calcium. Furthermore, interaction of recombinant SmC2P1 with bacterium-infected lymphocytes reduced bacterial survival. These results indicate that SmC2P1 is a functional protein that is involved in host immune defense against bacterial infection. (C) 2010 Elsevier Ltd. All rights reserved.

果实成熟衰老与抗病性的调控机制研究

　　果实为开花植物所特有的发育器官，在种子的成熟和传播过程中发挥着重要作用。同时，肉质果实中含有丰富的营养物质，包括纤维素、维生素、抗氧化剂等，成为人们饮食的重要组成部分。由于果实的成熟衰老和抗病性直接影响果品的质量和市场价值，因此，研究果实成熟衰老和抗病性的调控机制具有重要的理论意义和应用前景。本文主要利用蛋白质组学的方法，探讨外源化学物质抑制果实成熟衰老和诱导抗病性的调控机制。 1. 硅对果实的抗病性诱导：用硅酸钠（1%）处理采后的甜樱桃果实，再接种褐腐病原菌（Molinilia fracticola），置于20C下，观测贮藏期间果实的发病率，并分析硅处理后诱导的主要蛋白质及调控机制。研究结果表明：硅酸钠处理可显著抑制贮藏期间褐腐病的发生，其抑病机理与硅诱导PR-蛋白的表达，提高果实的抗氧化水平，减轻由病原菌侵染造成的氧化胁迫相关。同时，硅处理还能保护细胞骨架结构，有利于增强果实对病原菌入侵的抵抗力。 2. 水杨酸对果实的抗病性诱导：用水杨酸（SA，2mM）在果园处理三种成熟度的甜樱桃果实，然后接种青霉病原菌（Penicillium expansum）观察其发病情况，并取样分析参与抗病性应答的主要蛋白质及调控机制。试验结果表明：SA处理能显著降低青霉病的发病率和抑制病斑扩展，而且SA对低成熟度甜樱桃果实的抗性诱导效果更好。在八成熟的果实中，有5个热激蛋白和4个脱氢酶蛋白被SA诱导，这些蛋白参与了糖酵解和三羧酸循环。抗氧化蛋白和PR蛋白主要参与较低成熟度果实的抗性应答，而热激蛋白和脱氢酶在较高成熟度果实的抗性应答中更明显，SA诱导的抗性与代谢途径相关。 　　3. 草酸对果实的抗性诱导：用5mM的草酸处理冬枣果实后，接种青霉菌（P. expansum），观察果实发病情况，测定果实相关的生理指标，分析参与果实抗性应答的主要蛋白质及调控机制。结果表明：草酸能明显延缓冬枣果实的衰老，提高果实对青霉菌的抗性。草酸处理能抑制果实乙烯的释放量和呼吸强度，延缓叶绿素的降解，减少乙醇积累。利用蛋白质组学的研究方法证实了在25个参与了草酸处理应答的蛋白中，胱硫醚-β-合酶结构域包含蛋白（CBB domain-containing protein）和3个与光合作用相关蛋白[二磷酸核酮糖羧化酶/加氧酶（Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor），二磷酸核酮糖羧化酶/加氧酶大亚基结合蛋白（RuBisCO large subunit-binding protein subunit beta, chloroplast precursor），植物光系统Ⅱ放氧复合蛋白2（PSII oxygen-evolving complex protein 2）]的表达量上调，乙醇脱氢酶的表达量出现下调。草酸处理还提高了与乙烯合成前体相关蛋白的表达，抑制了ACC合成酶的活性。草酸提高果实抗病的机制与延缓果实成熟衰老和保持果实抗性有关。 4. 果实衰老的调控机制：采用高氧（100%）和低氧（2-3%）处理苹果果实，观察果实衰老的进程，并基于蛋白质组学的研究方法，探讨苹果果实衰老与线粒体蛋白质组的关系。结果表明，在苹果衰老过程中有22个蛋白的表达量发生变化，这些蛋白主要参与了三羧酸循环，电子传递，碳代谢和胁迫应答。高氧处理能诱导氧化胁迫，加速了果实的衰老。质谱鉴定结果证明：在高氧胁迫下，超氧化物歧化酶（manganese superoxide dismutase，MnSOD）和线粒体外膜通道蛋白（porin) 的表达量降低，MnSOD的活性受到抑制，由此提高了线粒体中超氧阴离子的含量，增加了蛋白质的氧化损伤。 此外，高氧处理改变了porin的功能，导致了线粒体膜的透势发生变化，从而引起外膜损伤。由此阐明了活性氧在果实的成熟衰老调控中的重要作用。

Xenopus RCOR2 (REST corepressor 2) interacts with ZMYND8, which is involved in neural differentiation

Regulation of neuronal gene expression is critical to nervous system development. REST (RE1-silencing transcription factor) regulates neuronal gene expression through interacting with a group of corepressor proteins including REST corepressors (RCOR). Here we show that Xenopus RCOR2 is predominantly expressed in the developing nervous system. Through a yeast two-hybrid screen, we isolated Xenopus ZMYND8 (Zinc finger and MYND domain containing 8) as an XRCOR2 interacting factor. XRCOR2 and XZMYND8 bind each other in co-immunoprecipitation assays and both of them can function as transcriptional repressors. XZMYND8 is co-expressed with XRCOR2 in the nervous system and overexpression of XZMYND8 inhibits neural differentiation in Xenopus embryos. These data reveal a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. (C) 2010 Elsevier Inc. All rights reserved.

Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia

The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene, GlTop 2 was identified. It is a single copy gene with a 4476 by long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a similar to 100 as longer central domain; a similar to 200 as shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the "amitochondriate" G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G. lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.

Origin and evolution of the RIG-I like RNA helicase gene family

Background: The DExD/H domain containing RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) of invading viruses. The RIG-I and MDA5 proteins differentially recognise conserved PAMPs in double stranded or single stranded viral RNA molecules, leading to activation of the interferon system in vertebrates. They share three core protein domains including a RNA helicase domain near the C terminus (HELICc), one or more caspase activation and recruitment domains (CARDs) and an ATP dependent DExD/H domain. The RIG-I/MDA5 directed interferon response is negatively regulated by laboratory of genetics and physiology 2 (LGP2) and is believed to be controlled by the mitochondria antiviral signalling protein (MAVS), a CARD containing protein associated with mitochondria. Results: The DExD/H containing RNA helicases including RIG-I, MDA5 and LGP2 were analysed in silico in a wide spectrum of invertebrate and vertebrate genomes. The gene synteny of MDA5 and LGP2 is well conserved among vertebrates whilst conservation of the gene synteny of RIG-I is less apparent. Invertebrate homologues had a closer phylogenetic relationship with the vertebrate RIG-Is than the MDA5/LGP2 molecules, suggesting the RIG-I homologues may have emerged earlier in evolution, possibly prior to the appearance of vertebrates. Our data suggest that the RIG-I like helicases possibly originated from three distinct genes coding for the core domains including the HELICc, CARD and ATP dependent DExD/H domains through gene fusion and gene/domain duplication. Furthermore, presence of domains similar to a prokaryotic DNA restriction enzyme III domain (Res III), and a zinc finger domain of transcription factor (TF) IIS have been detected by bioinformatic analysis. Conclusion: The RIG-I/MDA5 viral surveillance system is conserved in vertebrates. The RIG-I like helicase family appears to have evolved from a common ancestor that originated from genes encoding different core functional domains. Diversification of core functional domains might be fundamental to their functional divergence in terms of recognition of different viral PAMPs.

非洲爪蟾早期胚胎发育中PEDF和PEDF-R的功能以及vestigial-like家族表达图式的研究

PEDF 蛋白（Pigment epithelium-derived factor）又名“色素上皮源因子”或 “色素上皮衍生因子”，为一个多功能性分泌糖蛋白，前人研究表明PEDF 蛋白 具有神经保护性、免疫调节、抑制新生血管生成以及抑制肿瘤恶化等多种功能。 PEDF-R 是PEDF 的受体， 属于PNPLA2 （ Patatin-like phopholipase domain-containing 2 family）蛋白家族的一个新成员，PEDF 蛋白与其结合后会激 活PEDF-R 的磷脂酶A2 活性。本研究中，我们描述了非洲爪蟾PEDF 和PEDF-R 基因的表达图式及其在胚胎发育中的可能功能。RT-PCR 结果显示PEDF 是非母 源性表达，而PEDF-R 则是母源性表达的。原位杂交实验表明它们均在神经系统 中特异表达，但PEDF-R 的表达区域更加广泛，在鳃弓、眼泡和耳泡中也有表达。 通过mRNA 过表达和Morpholino(MO)阻断蛋白合成等手段发现，PEDF 功能获 得和功能缺失后胚胎几乎不受影响。然而PEDF-R 过表达后胚胎向注射一侧弯 曲，TUNEL 凋亡检测实验发现这些胚胎在注射一侧发生了凋亡。这两个基因神 经表达的特异性表明它们可能在早期神经发育中有重要功能。TUNEL 结果暗示 着PEDF-R 可能是一个与凋亡信号通路相关的受体。PEDF 功能获得和缺失并未 导致胚胎明显的表型，这表明PEDF 在非洲爪蟾中可能还存在其他的受体来行使 与PEDF-R 不同功能的途径。 果蝇的vestigial 基因编码一个转录辅助因子，在果蝇中只有一个成员，即 vestigial(vg)基因。在脊椎动物中有四个vestigial 同源基因，即vestigial-like 1,2,3,4_(vgl-1,2,3,4)。Vestigial 蛋白能作为辅助因子与果蝇中的Scalloped(Sd)蛋白 或者哺乳动物中的TEF 蛋白结合成复合体，通过Sd/TEF 蛋白的TEA/ATTS 结构 域与DNA 结合，从而调节下游基因的转录。本研究中，我们克隆了非洲爪蟾 vestigial-like 家族的四个成员，并对其在爪蟾胚胎发育过程中的表达进行研究。 RT-PCR 显示vgl-2 和vgl-3 是合子型表达的，vgl-1、vgl-4 则是母源性表达。原位 杂交显示：vgl-1 主要在神经管背部、耳泡和眼泡中表达；vgl-2 则是在肌肉、第 一二鳃弓、脊索中特异表达；vgl-3 神经胚时期在后脑有强的表达信号，从神经 胚后期到尾芽期后脑部位的表达几乎消失了，而在胚胎的头部以及神经管中开始 有微弱的表达；vgl-4 的表达较广泛，在神经管、眼泡、耳泡、肌肉以及脊索中 均有表达。在爪蟾中这四个成员的表达图式各不相同，提示它们有可能与其行使 组织特异性基因调控的功能相关，上述结果将有助于对vestigial-like 家族基因在 胚胎发育中的功能研究。

非洲爪蟾早期胚胎发育中PEDF和PEDF-R的功能以及vestigial-like家族表达图式的研究

PEDF 蛋白（Pigment epithelium-derived factor）又名“色素上皮源因子”或 “色素上皮衍生因子”，为一个多功能性分泌糖蛋白，前人研究表明PEDF 蛋白 具有神经保护性、免疫调节、抑制新生血管生成以及抑制肿瘤恶化等多种功能。 PEDF-R 是PEDF 的受体， 属于PNPLA2 （ Patatin-like phopholipase domain-containing 2 family）蛋白家族的一个新成员，PEDF 蛋白与其结合后会激 活PEDF-R 的磷脂酶A2 活性。本研究中，我们描述了非洲爪蟾PEDF 和PEDF-R 基因的表达图式及其在胚胎发育中的可能功能。RT-PCR 结果显示PEDF 是非母 源性表达，而PEDF-R 则是母源性表达的。原位杂交实验表明它们均在神经系统 中特异表达，但PEDF-R 的表达区域更加广泛，在鳃弓、眼泡和耳泡中也有表达。 通过mRNA 过表达和Morpholino(MO)阻断蛋白合成等手段发现，PEDF 功能获 得和功能缺失后胚胎几乎不受影响。然而PEDF-R 过表达后胚胎向注射一侧弯 曲，TUNEL 凋亡检测实验发现这些胚胎在注射一侧发生了凋亡。这两个基因神 经表达的特异性表明它们可能在早期神经发育中有重要功能。TUNEL 结果暗示 着PEDF-R 可能是一个与凋亡信号通路相关的受体。PEDF 功能获得和缺失并未 导致胚胎明显的表型，这表明PEDF 在非洲爪蟾中可能还存在其他的受体来行使 与PEDF-R 不同功能的途径。 果蝇的vestigial 基因编码一个转录辅助因子，在果蝇中只有一个成员，即 vestigial(vg)基因。在脊椎动物中有四个vestigial 同源基因，即vestigial-like 非洲爪蟾早期胚胎发育中PEDF 和PEDF-R 的功能以及vestigial-like 家族表达图式的研究 2 1,2,3,4_(vgl-1,2,3,4)。Vestigial 蛋白能作为辅助因子与果蝇中的Scalloped(Sd)蛋白 或者哺乳动物中的TEF 蛋白结合成复合体，通过Sd/TEF 蛋白的TEA/ATTS 结构 域与DNA 结合，从而调节下游基因的转录。本研究中，我们克隆了非洲爪蟾 vestigial-like 家族的四个成员，并对其在爪蟾胚胎发育过程中的表达进行研究。 RT-PCR 显示vgl-2 和vgl-3 是合子型表达的，vgl-1、vgl-4 则是母源性表达。原位 杂交显示：vgl-1 主要在神经管背部、耳泡和眼泡中表达；vgl-2 则是在肌肉、第 一二鳃弓、脊索中特异表达；vgl-3 神经胚时期在后脑有强的表达信号，从神经 胚后期到尾芽期后脑部位的表达几乎消失了，而在胚胎的头部以及神经管中开始 有微弱的表达；vgl-4 的表达较广泛，在神经管、眼泡、耳泡、肌肉以及脊索中 均有表达。在爪蟾中这四个成员的表达图式各不相同，提示它们有可能与其行使 组织特异性基因调控的功能相关，上述结果将有助于对vestigial-like 家族基因在 胚胎发育中的功能研究。

来自易变山羊草抗禾谷孢囊线虫基因的克隆与序列分析

禾谷孢囊线虫（Heterodera avenae）是严重危害禾谷类作物的病原线虫之一,它广泛分布于澳大利亚、欧洲、北美、印度和中国等世界主要小麦产区,使作物严重减产,造成巨大的经济损失。目前最有效的防治措施之一是将外源抗性基因导入栽培小麦(Triticum aestivum L.)，培育抗禾谷孢囊线虫的新品种。但迄今为止抗禾谷孢囊线虫基因克隆研究的相关报道却很少。 本实验根据此前从抗禾谷孢囊线虫材料E-10扩增得到的与来自节节麦（Aegilops tauschii）的抗禾谷孢囊线虫基因Cre3高度同源的序列Rccn4,设计出三条嵌套引物,采用SON-PCR(single oligonucleotide nested PCR)方法,从E-10基因组DNA中得到一个长为1264 bp的扩增产物(命名为Rccn-L),测序比对结果显示,这一序列将Rccn4的3’端延伸了1209 bp,与抗禾谷孢囊线虫Cre3基因核苷酸同源性为86﹪，核苷酸编码区长1026 bp，含一个不完整的开放阅读框,一个终止密码子，没有起始密码子和内含子结构,编码一个342个氨基酸残基的蛋白质。该蛋白质等电点为5.19，分子量为38112.6Da。从序列的第113位开始到第332位是NBS-LRR类抗病性基因LRR区,呈现XXLXXLXXL重复。LRR编码区内亮氨酸残基的含量达17﹪，与抗禾谷孢囊线虫Cre3基因LRR编码区的核苷酸和氨基酸同源性分别为89﹪和78﹪。本实验首次将SON-PCR成功地运用于植物基因克隆，为植物基因克隆提供了又一有效方法。 此外,还根据Cre3基因及其他的NBS-LRR类植物抗性基因的NBS和LRR区保守序列设计了两对特异性引物，从禾谷孢囊线虫抗性材料易变山羊草基因组DNA中扩增到两个相应的目标条带。测序分析结果表明，它们的长度分别为532bp和1175bp，构成了一个有32bp的共同序列的NBS-LRR编码区。其序列总长为1675bp（命名为RCCN），含有一个不完整的开放阅读框，没有起始密码子、终止密码子和内含子结构。其中编码序列为1673bp，可编码一个557个氨基酸的蛋白质，等电点（pI）为5.39，分子量为63537.5Da。与Cre3的核苷酸和氨基酸同源性分别为87.8﹪和77﹪。RCCN氨基酸序列中含有已知抗病基因NBS区域的几个保守模体：kinase2区的ILDD、kinase3的（ⅰ）ESKILVTTRSK，（ⅱ）KGSPLAARTVGG，（ⅲ）RRCFAYCS及EGF。RCCN NBS区与Cre3 NBS区的核苷酸和氨基酸的同源性分别为96.4﹪和94﹪。从氨基酸序列的274位到548位为LRR保守区，呈现不规则的aXXLXXLXXL（其中a代表I，V，L，F或M）重复，其中亮氨酸的含量为15.6﹪。该区域与Cre3的LRR区的核苷酸和氨基酸同源性分别为80.8﹪和74﹪。推测该序列可能为一个抗禾谷孢囊线虫的新基因。 本文对抗禾谷孢囊线虫基因的克隆研究，为进一步克隆基因全序列，探索其结构与功能，和研究该基因表达与调控提供了关键信息。同时也为通过基因工程途径将抗性基因向优良小麦品种高效、定向转移，最终培育出小麦抗禾谷孢囊线虫新品种奠定了基础。 Cereal cyst nematode (CCN) is a damaging pathogen of broad acre cereal crops in Australia, Europe, North America, India and China. It affects wheat, barley, oat and triticale and causes yield loss of up to 80%. At present, Transferring resistance genes against CCN into wheat cultivars and breeding varieties are considered one of the most effective methods for controlling the CCN. However, there are very limited reports concerning the cloning studies of resistance genes against the cereal cyst nematode. According to the sequence of Rccn4 which had high similarity to the nucleotide binding site (NBS) coding region of cereal cyst nematode resistance gene, Cre3， We designed three 3’ nested primers. Using single oligonucleotide nested PCR (SON-PCR) we successfully amplified one band, Rccn-L, of 1264bp from E-10 which is the wheat-Ae.variabilis translocation line containing the cereal cyst nematode resistance gene of Ae.variabilis. We found that this band of interesting is the 3’ flanking sequence of 1209bp in size of Rccn4. The coding region was 1026bp, which contained an incomplete open reading frame and a terminator codon, without initiation codon and intron, encoding a peptide of 342 amino acid residues, and shared 86﹪nucleotide sequence identity with Cre3. This peptide had a conserved LRR domain, containing the imperfect repeats,XXLXXLXXL, which contains 17﹪ leucine residues and shares, respectively, 89﹪ nucleotide sequence and 78﹪ amino acid sequence identity with the LRR sequence of Cre3 locus. This research firstly used SON-PCR in the research of plant genome successfully, which indicated that SON-PCR is another method of cloning plant gene. At the same time, According to the conversed motif of NBS and LRR region of cereal cyst nematode resistance gene Cre3 from wild wheat (Triticum tauschlii L.) and the known NBS-LRR group resistance genes, we designed two pairs of specific primers for NBS and LRR region respectively. One band of approximately 530bp was amplified using the specific primers for conversed NBS region and one band of approximately 1200bp was amplified with the specific primers for conversed LRR region. After sequencing, we found that these two sequences included 32bp common nucleotide sequence and have 1675 bp in total, which was registered as RCCN in the Genbank. RCCN contained a NBS-LRR domain and an incomplete open reading frame without initiation codon, terminator codon and inxon. Its exon encodes a peptide of 557 amino acid residues. The molecular weight of the protein from the amino acid was 63.537 KDa. The amino acid sequence of RCCN contained conserved motif: ILDD, ESKILVTTRSK, KGSPLAARTVGG, RRCFAYCS, EGF，LRR. RCCN shares 87.8﹪ nucleotide sequence and 77﹪ amino acid sequence identity with cereal cyst nematode gene Cre3. It might be a novel cereal cyst nematode resistance gene. These research results of cloning the resistance genes against cereal cyst nematode bring a great promise for transferring resistance genes into wheat cultivars and breeding new wheat varieties against cereal cyst nematode by gene engineering. And these results also lay the hard foundation for the expressing researches of these genes.

First molluscan TNFR homologue in Zhikong scallop: Molecular characterization and expression analysis

Tumor necrosis factor receptors (TNFRs) are a superfamily of proteins characterized by the unique cysteine-rich domain (CRD) and their important roles in diverse physiological and pathological events such as inflammation, apoptosis, autoimmunity and organogenesis. The first member of the molluscan TNFR family, designated as CfTNFR, was identified from Zhikong scallop Chlamys farreri by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of CfTNFR was of 1334 bp, consisting of a 5' UTR of 17 bp, a 3'UTR of 69 by with a poly (A) tail, and an open reading frame (ORE) of 1248 by encoding a polypeptide of 415 amino acids with a theoretical isoelectric point of 8.33 and predicted molecular weight of 47.07 kDa. There were a signal peptide, a CRD, a transmembrane region and a death domain in the deduced amino acid sequence of CfTNFR, suggesting that it was a typical type 1 membrane protein. The high identities (22-40%) of CfTNFR with other TNFR superfamily members indicated that CfTNFR should be a member of TNFR superfamily, and moreover, it should be the first death domain-containing TNFR found in invertebrates. Phylogenetic analysis revealed that CfTNFR was closely related to TNFR-like proteins from Strongylocentrotus purpuratus, Drosophila melanogaster and Ciona intestinalis, and they formed a separate branch apart from vertebrate TNFRs. The spatial expression of CfTNFR transcripts in healthy and bacteria challenged scallops was examined by quantitative real-time PCR. CfTNFR transcripts could be detected in all tested tissues, including haemocytes, gonad, gill, mantle and hepatopancreas, and significantly up-regulated in the tissues of gonad, gill, mantle and hepatopancreas after Listonella anguillarum challenge, indicating that CfTNFR was constitutive and inducible acute-phase protein involved in immune defence. The present results suggested the existence of the TNFR-like molecules and TNF-TNFR system in low invertebrates, and provided new insights into the role of CfTNFR in scallop innate immune responses to invading microorganisms. (C) 2009 Elsevier Ltd. All rights reserved.