非洲爪蟾短型肽聚糖识别蛋白基因的克隆与鉴定

采用生物信息学方法首次对非洲爪蟾短型肽聚糖识别蛋白(xePGRP-S)基因进行了克隆,并对其在胚胎发育和成年爪蟾各组织中的表达状况进行了分析。xePGRP-ScDNA全长720bp,开放阅读框为549bp,编码182个氨基酸。序列比对显示xePGRP-S与其他物种PGRP-S的序列相似性在42.4%-50.5%之间。RT-PCR显示在非洲爪蟾胚胎发育至3d时可以明显检测到xePGRP-S的表达,之后呈持续性表达,且在所检测的心、肝、脾、肺、肾、肠和胃这7种组织器官中呈组成型表达。       

非洲爪蟾BAFF及其信号通路相关基因的比较生物信息学分析

目的:对非洲爪蟾BAFF和BAFF信号通路相关基因进行了分析.方法:采用生物信息学方法对两栖类重要的模式生物-非洲爪蟾的基因组和EST数据库进行分析.结果:非洲爪蟾BAFF cDNA全长为557 bp,编码218个氨基酸.与人BAFF序列相似性为37.5％.该文一共得到了14个BAFF信号通路相关基因.通过与人BAFF信号通路进行比较,对非洲爪蟾这14个BAFF信号通路相关基因进行了分析.结论:BAFF和BAFF信号通路在进化过程中较为保守,这为进一步研究低等脊椎动物BAFF功能和信号通路具有重要的指导作用.     

非洲爪蟾基因MGC64236的克隆及初步分析

MGC64236基因是本实验室用脐静脉内皮细胞免疫的兔血清筛选非洲爪蟾cDNA文库而鉴定的一个功能未知的基因.本研究提取非洲爪蟾受精卵总RNA通过RT-PCR得到基因MGC64236的开放读码框651 bp、编码202个氨基酸;运用生物信息学研究工具进行分析,发现该基因编码的蛋白有3个潜在的跨膜域,有一保守的结构域DUF1370, 可能通过其胞内部分的磷酸化机制在介导细胞内外的信号转导中发挥重要作用;在非洲爪蟾胚胎各个发育时期用RT-PCR检测该基因的表达情况,发现在非洲爪蟾胚胎发育的几个重要时期该基因都有高表达,而在成体则特异地表达于脑和眼等神经组织;构建绿色荧光融合蛋白真核表达载体并转染HEK293细胞, 对MGC64236蛋白的亚细胞定位,发现MGC64236蛋白比较特异地表达在细胞膜.     

非洲爪蟾IL-6基因的克隆及生物信息学分析

生物信息学作为一门新兴学科,已经应用到生命科学、临床医药、工农业等方面。白细胞介素-6(IL-6)是机体重要的免疫因子,但在两栖类中未见报道。采用生物信息学方法对两栖类模式动物非洲爪蟾IL-6进行分析。以人IL-6基因对非洲爪蟾数据库进行搜索、分析,并采用RT-PCR方法对所得序列进行验证。结果表明,非洲爪蟾IL-6基因位于scaffold_52基因架上,具有保守的IL-6家族基序。采用生物信息新方法进行不同物种的免疫基因挖掘、克隆,是一种有效的方法。     

非洲爪蟾GATA-1转录因子与爪蟾发育

GATA－1是GATA结合蛋白（GATA－binding protein）家族的成员之一,正向调节红细胞特异性基因的表达,是红系终末分化所必需的因子。与其他物种不同的是,非洲爪蟾GATA－1转录因子具有两业型,两者结构极为相似,但存在功能上的差异,非洲爪蟾GATA－1转录因子在爪蟾发育过程中起着重要的调节作用。     

中华大蟾蜍Mest基因的cDNA克隆和表达分析

Mest基因是一种印记基因,在人、小鼠以及其他的哺乳动物和有花植物中都有研究报道。为了更好地研究该基因的功能和进化特点,利用RACE法获得了中华大蟾蜍Mest基因(BgMest)的cDNA全长序列(1 325 bp),它包含一个完整的ORF,可编码326个氨基酸的多肽(GenBank登陆号:ABQ10905)。多肽链中包含一个典型的α/β水解酶折叠结构域,其在氨基酸水平上与热带爪蟾和一些哺乳动物分别存在86%和70%～80%的相似性。进化树分析显示Mest基因为单系起源。RT-PCR显示,BgMest基因在精巢、卵巢、肝、肾、脑、胃和肺中都有表达,并且该基因在序列、表达模式以及蛋白产物的高级结构的高度保守性都说明它在两栖类生物中是保守的。但是在对哺乳动物以及一些脊椎动物的印记基因进行进化分析时,发现它们具有不同的起源。     

细粒棘球绦虫水通道蛋白基因家族成员密码子偏好性分析

水通道蛋白(aquaporin, AQP)是一种主要内在蛋白家族成员,具有通透水及其他小分子溶质的功能,参与虫体渗透稳态、物质转运等过程。本研究运用CodonW、SPSS等生物信息学软件分析细粒棘球绦虫(Echinococcus granulosus)水通道蛋白基因家族成员(EgAQPs)的密码子使用偏好性,并与非洲爪蟾(Xenopus laevis)卵母细胞、酵母(Saccharomyces cerevisiae)进行密码子偏好性比较,以期找到EgAQPs最合适的外源表达系统。结果表明EgAQPs密码子选用偏好性普遍较弱,偏好以C/G作为结尾。在密码子使用频率上,EgAQPs与非洲爪蟾卵母细胞的差异高于酵母,表明酵母表达系统可能更适合于EgAQPs表达。若要进一步提高EgAQPs在非洲爪蟾卵母细胞或酵母中的表达水平,尚需对其密码子进行优化。     

Sox1基因在爪蟾早期发育中的时空表达图式

克隆了非洲爪蟾的Sox1基因并研究了它在非洲爪蟾早期发育过程中的时空表达图式,比较了Sox1—3基因在发育的脑和眼中的表达图式。序列比对分析显示Sox1—3蛋白在其HMG框结构域具有高度的保守性。通过RT-PCR方法分析了Sox1基因在爪蟾早期不同发育时段的表达情况,结果显示Sox1基因从未受精卵到尾芽期均有表达,但表达强度有所差异。原位杂交结果显示,在早期卵裂阶段和囊胚期,Sox1基因主要在动物极表达;从神经板期开始,Sox1基因主要在中枢神经系统和眼原基中表达。在蝌蚪期,Sox1与Sox2、Sox3在脑部和眼睛的表达区域有所不同。对于爪蟾Sox1基因时空表达图式的研究将有助于阐明SoxB1基因家族在脊椎动物神经系统发生过程中的作用。     

免疫代价不是非洲爪蟾语音性信号真实度的维持机制

性选择理论认为,雄性性信号的真实度是雌性根据雄性表型质量进行配偶选择的前提。而维持这种真实度的机制普遍被认为是基于障碍原理,即性信号的表达必须付出与身体质量关联的存活代价,性信号与存活代价在个体内呈负的权衡关系,在个体间呈正相关关系。已有研究表明,免疫能力是表达性信号潜在的存活代价。但免疫代价在维持无尾两栖类语音性信号真实度中的作用尚不清楚。以非洲爪蟾为研究对象,在能量限制条件下采用灭活的大肠杆菌激活其免疫系统,测定鸣叫时长及相关繁殖行为表现,检验免疫能力与语音性信号表达间是否存在生理权衡。结果表明,免疫激活和能量限制对非洲爪蟾鸣叫时长和趋声行为都无影响;温度变化对鸣叫时长有显著作用。这些结果提示:非洲爪蟾语音性信号表达和免疫能力间不存在生理权衡,免疫代价不是非洲爪蟾语音性信号真实度的维持机制。     

非洲爪蟾PAPC多克隆抗体的制备及其特异性鉴定

非洲爪蟾ParaxialProtocadherin(PAPC)是一个在爪蟾Spemann组织者特异表达的膜蛋白.它在爪蟾原肠运动阶段的汇聚延伸运动和体节发生阶段的体节边界形成,以及早期听泡的形态发生和细胞特化过程中都有重要的作用.为了研究PAPC基因在早期胚胎发育过程中的表达及其生物学功能,需要制备PAPC抗体.应用谷胱甘肽S-转移酶(glutathioneStransferase,GST)表达系统表达GST-PAPC融合蛋白,亲和纯化后用以免疫新西兰大白兔,获得PAPC多克隆抗体.免疫印迹分析发现,以1∶3000稀释的该多克隆抗体为一抗时,能够在转染了全长PAPC质粒的HEK293T细胞的蛋白质抽提物中,特异地识别出150ku的印迹条带.同时,GST-PAPC融合蛋白可以竞争性抑制该抗体对全长PAPC质粒转染细胞的蛋白质抽提物的特异性条带.用1∶500稀释的该抗体为一抗进行免疫荧光分析时,发现,PAPC多克隆抗体能够识别在HEK293T细胞中过表达以及爪蟾动物极细胞中过表达的PAPC蛋白,荧光信号定位在细胞膜上.免疫印迹分析证明,PAPC抗体能够识别爪蟾胚胎中内源表达的PAPC蛋白.     

INVOLVEMENT OF PEPTIDOGLYCAN RECOGNITION PROTEIN L6 IN ACTIVATION OF IMMUNE DEFICIENCY PATHWAY IN THE IMMUNE RESPONSIVE SILKWORM CELLS

The immune deficiency (Imd) signaling pathway is activated by Gram‐negative bacteria for producing antimicrobial peptides (AMPs). In Drosophila melanogaster, the activation of this pathway is initiated by the recognition of Gram‐negative bacteria by peptidoglycan (PGN) recognition proteins (PGRPs), PGRP‐LC and PGRP‐LE. In this study, we found that the Imd pathway is involved in enhancing the promoter activity of AMP gene in response to Gram‐negative bacteria or diaminopimelic (DAP) type PGNs derived from Gram‐negative bacteria in an immune responsive silkworm cell line, Bm‐NIAS‐aff3. Using gene knockdown experiments, we further demonstrated that silkworm PGRP L6 (BmPGRP‐L6) is involved in the activation of E. coli or E. coli‐PGN mediated AMP promoter activation. Domain analysis revealed that BmPGRP‐L6 contained a conserved PGRP domain, transmembrane domain, and RIP homotypic interaction motif like motif but lacked signal peptide sequences. BmPGRP‐L6 overexpression enhances AMP promoter activity through the Imd pathway. BmPGRP‐L6 binds to DAP‐type PGNs, although it also binds to lysine‐type PGNs that activate another immune signal pathway, the Toll pathway in Drosophila. These results indicate that BmPGRP‐L6 is a key PGRP for activating the Imd pathway in immune responsive silkworm cells.     

Crystal structure of peptidoglycan recognition protein SA in Apis mellifera (Hymenoptera: Apidae)

Peptidoglycan recognition protein SA (PGRP‐SA) is a key pattern recognition receptor in the insect innate immune system. PGRP‐SA can bind to bacterial PGN and activate the Toll pathway, which triggers the expression and release of antimicrobial peptides to prevent bacterial infection. Here, we report the first structure of Apis mellifera PGRP‐SA from Hymenoptera at 1.86 Å resolution. The overall architecture of Am‐PGRP‐SA was similar to the Drosophila PGRP‐SA; however, the residues involved in PGN binding groove were not conserved, and the binding pocket was narrower. This structure gives insight into PGN binding characteristics in honeybees.     

Molecular cloning and characterization of a short type peptidoglycan recognition protein (CfPGRP-S1) cDNA from Zhikong scallop Chlamys farreri

Peptidoglycan recognition protein (PGRP) specifically binds to peptidoglycan and plays a crucial role in the innate immune responses as a pattern recognition receptor (PRR). The cDNA of a short type PGRP was cloned from scallop Chlamys farreri (named CfPGRP-S1) by homology cloning with degenerate primers, and confirmed by virtual Northern blots. The full length of CfPGRP-S1 cDNA was 1073 bp in length, including a 5' untranslated region (UTR) of 59 bp, a 3' UTR of 255 bp, and an open reading frame (ORF) of 759 bp encoding a polypeptide of 252 amino acids with an estimated molecular mass of 27.88 kDa and a predicted isoelectric point of 8.69. BLAST analysis revealed that CfPGRP-S1 shared high identities with other known PGRPs. A conserved PGRP domain and three zinc-binding sites were present at its C-terminus. The temporal expression of CfPGRP-S1 gene in healthy, Vibrio anguillarum-challenged and Micrococcus lysodeikticus-challenged scallops was measured by RT-PCR analysis. The expression of CfPGRP-S1 was upregulated initially in the first 12 h or 24 h either by M. lysodeikticus or V. anguillarum challenge and reached the maximum level at 24 h or 36 h, then dropped progressively, and recovered to the original level as the stimulation decreased at 72 h. There was no significant difference between V. anguillarum and M. lysodeikticus challenge. The results indicated that the CfPGRP-S1 was a constitutive and inducible acute-phase protein which was involved in the immune response against bacterial infection.     

Mammalian peptidoglycan recognition protein binds peptidoglycan with high affinity, is expressed in neutrophils, and inhibits bacterial growth

Peptidoglycan recognition protein (PGRP) is conserved from insects to mammals. In insects, PGRP recognizes bacterial cell wall peptidoglycan (PGN) and activates prophenoloxidase cascade, a part of the insect antimicrobial defense system. Because mammals do not have the prophenoloxidase cascade, its function in mammals is unknown. However, it was suggested that an identical protein (Tag7) was a tumor necrosis factor-like cytokine. Therefore, the aim of this study was to identify the function of PGRP in mammals. Mouse PGRP bound to PGN with fast kinetics and nanomolar affinity (K(d) = 13 nm). The binding was specific for polymeric PGN or Gram-positive bacteria with unmodified PGN, and PGRP did not bind to other cell wall components or Gram-negative bacteria. PGRP mRNA and protein were expressed in neutrophils and bone marrow cells, but not in spleen cells, mononuclear cells, T or B lymphocytes, NK cells, thymocytes, monocytes, and macrophages. PGRP was not a PGN-lytic or a bacteriolytic enzyme, but it inhibited the growth of Gram-positive but not Gram-negative bacteria. PGRP inhibited phagocytosis of Gram-positive bacteria by macrophages, induction of oxidative burst by Gram-positive bacteria in neutrophils, and induction of cytokine production by PGN in macrophages. PGRP had no tumor necrosis factor-like cytotoxicity for mammalian cells, and it was not chemotactic on its own or in combination with PGN. Therefore, mammalian PGRP binds to PGN and Gram-positive bacteria with nanomolar affinity, is expressed in neutrophils, and inhibits growth of bacteria.     

NMR structure of Citrobacter freundii AmpD,comparison with bacteriophage T7 lysozyme and homology with PGRP domains

AmpD is a bacterial amidase involved in the recycling of cell-wall fragments in Gram-negative bacteria. Inactivation of AmpD leads to derepression of beta-lactamase expression, presenting a major pathway for the acquisition of constitutive antibiotic resistance. Here, we report the NMR structure of AmpD from Citrobacter freundii (PDB accession code 1J3G). A deep substrate-binding pocket explains the observed specificity for low molecular mass substrates. The fold is related to that of bacteriophage T7 lysozyme. Both proteins bind zinc at a conserved site and require zinc for amidase activity, although the enzymatic mechanism seems to differ in detail. The structure-based sequence alignment identifies conserved features that are also conserved in the eukaryotic peptidoglycan recognition protein (PGRP) domains, including the zinc-coordination site in several of them. PGRP domains thus belong to the same fold family and, where zinc-binding residues are conserved, may have amidase activity. This hypothesis is supported by the observation that human serum N-acetylmuramyl-L-alanine amidase seems to be identical with a soluble form of human PGRP-L.     

A peptidoglycan recognition protein from Sciaenops ocellatus is a zinc amidase and a bactericide with a substrate range limited to Gram-positive bacteria

Peptidoglycan recognition proteins (PGRPs) are a family of innate immune molecules that recognize bacterial peptidoglycan. PGRPs are highly conserved in invertebrates and vertebrates including fish. However, the biological function of teleost PGRP remains largely uninvestigated. In this study, we identified a PGRP homologue, SoPGLYRP-2, from red drum (Sciaenops ocellatus) and analyzed its activity and potential function. The deduced amino acid sequence of SoPGLYRP-2 is composed of 482 residues and shares 46-94% overall identities with known fish PGRPs. SoPGLYRP-2 contains at the C-terminus a single zinc amidase domain with conserved residues that form the catalytic site. Quantitative RT-PCR analysis detected SoPGLYRP-2 expression in multiple tissues, with the highest expression occurring in liver and the lowest expression occurring in brain. Experimental bacterial infection upregulated SoPGLYRP-2 expression in kidney, spleen, and liver in time-dependent manners. To examine the biological activity of SoPGLYRP-2, purified recombinant proteins representing the intact SoPGLYRP-2 (rSoPGLYRP-2) and the amidase domain (rSoPGLYRP-AD) were prepared from Escherichia coli. Subsequent analysis showed that rSoPGLYRP-2 and rSoPGLYRP-AD (i) exhibited comparable Zn²⁺-dependent peptidoglycan-lytic activity and were able to recognize and bind to live bacterial cells, (ii) possessed bactericidal effect against Gram-positive bacteria and slight bacteriostatic effect against Gram-negative bacteria, (iii) were able to block bacterial infection into host cells. These results indicate that SoPGLYRP-2 is a zinc-dependent amidase and a bactericide that targets preferentially at Gram-positive bacteria, and that SoPGLYRP-2 is likely to play a role in host innate immune defense during bacterial infection.     

小菜蛾PGRP-S2基因的克隆表达及功能分析

肽聚糖识别蛋白(peptidoglycan recognition protein,PGRP)对于昆虫来说是一种高度保守的病原识别蛋白。为阐明PGRP-S2在小菜蛾Plutella xylostella抵抗病原微生物过程中的作用,本研究结合RT-PCR和RACE技术克隆得到小菜蛾PGRP-S2基因的cDNA全长序列,命名为PGRP-S2(GenBank登录号:MG570190)。生物信息学分析结果表明,PGRP-S2的开放阅读框为588 bp,编码195个氨基酸;蛋白质预测分子量为21.46 kDa,理论等电点为8.46;编码蛋白具有PGRP超家族保守结构域和酰胺酶结构域,是典型的肽聚糖识别蛋白,包含一条信号肽,不存在跨膜结构;同源序列比对和系统进化树分析表明PGRP-S2与家蚕Bombyx mori的BmPGRP-S 1进化距离最近。利用大肠杆菌Escherichia coli BL21(DE3)高效表达重组蛋白PxPGRP-S2,利用倒置显微镜及平板涂布观察重组蛋白对大肠杆菌E.coli和金黄色葡萄球菌Staphylococcus aureus的作用,结果表明PxPGRP-S2蛋白能够与两种细菌发生结合并凝集细菌,但不具备直接杀菌功能。本研究为进一步研究基于PGRP-S2介导的小菜蛾免疫防御反应提供基础。     

The differentially spliced mouse tagL gene,homolog of tag7/PGRP gene family in mammals and Drosophila,can recognize Gram-positive and Gram-negative bacterial cell wall independently of T phage lysozyme homology domain

Tag7/PGRP, a recently characterized antimicrobial protein, is conserved from insects to mammals. Recently its involvement in Toll signalling in Drosophila was demonstrated. A number of genes representing a new family homologous to PGRP were identified in Drosophila and human. Here we describe a splicing pattern of the tagL gene, mouse member of tag7/PGRP family. Some of the identified splice variants lacked characteristics for the family T phage lysozyme homology domain (also known as PGRP domain). Accordingly to the predicted transmembrane domains, mouse TagL may be secreted as inducible proteins or retained on intracellular membranes. All detected splice variant isoforms of TagL bound Gram-positive, Gram-negative bacteria and peptidoglycan. This binding did not depend on the presence of T phage lysozyme homology domain but was associated with the C-terminal portion of the polypeptides. Thus, this variety of isoforms of a single gene may play a role in circulating bacteria recognition in mammals.     

The Drosophila peptidoglycan-recognition protein LF interacts with peptidoglycan-recognition protein LC to downregulate the Imd pathway

The peptidoglycan (PGN)‐recognition protein LF (PGRP‐LF) is a specific negative regulator of the immune deficiency (Imd) pathway in Drosophila. We determine the crystal structure of the two PGRP domains constituting the ectodomain of PGRP‐LF at 1.72 and 1.94 Å resolution. The structures show that the LFz and LFw domains do not have a PGN‐docking groove that is found in other PGRP domains, and they cannot directly interact with PGN, as confirmed by biochemical‐binding assays. By using surface plasmon resonance analysis, we show that the PGRP‐LF ectodomain interacts with the PGRP‐LCx ectodomain in the absence and presence of tracheal cytotoxin. Our results suggest a mechanism for downregulation of the Imd pathway on the basis of the competition between PRGP‐LCa and PGRP‐LF to bind to PGRP‐LCx.     

A pattern recognition protein for peptidoglycan. Cloning the cDNA and the gene of the silkworm, Bombyx mori

Peptidoglycan recognition protein (PGRP) specifically binds to peptidoglycan and is considered to be one of the pattern recognition proteins in the innate immunity of insect. The PGRP is an essential component for peptidoglycan to trigger the prophenoloxidase cascade that is now recognized to be an important insect defense mechanism. We cloned cDNA encoding PGRP from the silkworm fat body cDNA library. Northern blot analysis showed that the PGRP gene is constitutively expressed in the fat body, epithelial cell, and hemocytes of naive silkworms. Furthermore, a bacterial challenge intensified the gene expression, with the maximal period being from 6 to 36 h after infection. The upstream sequence of the cloned PGRP gene was shown to contain putative cis-regulatory elements similar to the NF-kappaB-like element, interferon-response half-element, and GATA motif element, which have been found in the promoters of the acute phase protein genes of mammals and insects. A homology search revealed that the homologs of silkworm PGRP are present in mice, nematodes, and bacteriophages. This suggests that the recognition of peptidoglycan as foreign is effected in both vertebrates and invertebrates by PGRP homologs with an evolutionally common origin.