异育银鲫c型溶菌酶全长cDNA序列的生物信息学分析及其组织表达分析

利用RACE及克隆等方法获得了异育银鲫（Carassius auratus gibelio）c型溶菌酶基因全长cDNA序列．序列分析表明,所克隆的异育银鲫溶菌酶的cDNA全长751 bp,包括溶菌酶基因开放阅读框（ORF）438 bp,5′ 非编码区（UTR）为109 bp和3′ UTR为204 bp．438 bp ORF共编码146个氨基酸,其成熟肽的分子量预测值为14　543.6,理论等电点为8.86．通过ClustalW软件,将异育银鲫和其它多个物种c型溶菌酶的氨基酸序列进行多序列比对发现,所克隆的异育银鲫溶菌酶编码的氨基酸序列中存在c型溶菌酶的活性中心（Glu53和Asp69）,且与活性位点相邻的氨基酸序列高度保守．同时,8个保守的半胱氨酸残基也与其它物种的c型溶菌酶相一致．结合BLASTN分析的结果,可以确认所获得的异育银鲫溶菌酶cDNA序列属于c型溶菌酶．异育银鲫c型溶菌酶和人c型溶菌酶（pdb 1at6_）在蛋白质序列上有50%相似性,其三维（3-D）结构非常类似．通过氨基酸空间位置比较发现,两者具有类似的酶活中心,异育银鲫c型溶菌酶只能形成3个二硫键,比人少1个．荧光定量RT-PCR检测和溶菌酶活性测定显示,异育银鲫头肾和脾脏c型溶菌酶mRNA的表达量约为肝胰脏的2.9 倍和1.7 倍,异育银鲫头肾和脾脏的溶菌酶活性约为肝胰脏的6.2 倍和4倍．     

大黄鱼KLF6基因分子克隆和特征分析

KLF6具有抗细胞增殖的特性,在抑制肿瘤细胞方面起着重要作用.在获得KLF6基因EST序列的基础上,克隆到了KLF6基因,全长1185 bp,其中5′端198 bp,3′端333 bp,开放阅读框654 bp,编码217个氨基酸.与KLF转录因子家族其它成员一样,大黄鱼KLF6的C-端含有3个连续的C2H2型锌指结构域.其氨基酸序列高度保守,与其它鱼类的同源性在90%以上.在检测的大黄鱼骨骼肌、肝脏、眼、脑、脾、心、鳃、肠和肾等9种组织中,KLF6都有不同程度的表达,其中肾、肝脏、鳃、脾脏和脑等组织中的表达量较高.KLF6表达范围的广泛性提示其在多种组织中参与细胞功能活动的调控.     

陆封型和洄游型香鱼体肾组织的蛋白质组学分析

香鱼（Plecoglossusaltivelis）是典型的降海洄游鱼类,由于地理原因,一些香鱼在繁殖季无法回到海中产卵,形成陆封型香鱼。陆封型和洄游型香鱼相比,其体型明显偏小。鱼类的体肾组织可以调控渗透压,从而影响生长,因此我们采用蛋白质组学的方法研究陆封型和洄游型香鱼体肾组织蛋白质组的差异。双向电泳（2一DE）分析筛选到25个差异表达蛋白点,质谱分析成功鉴定出21个蛋白。与洄游型香鱼相比,陆封型香鱼体肾组织中NADH脱氢酶、异柠檬酸脱氢酶、Or．．微管蛋白、热适应相关蛋白65（Wap65）、热休克蛋白60（HSP60）、丙酮酸脱氢酶（E1）、碳酸酐酶、烯醇酶和乳酸脱氢酶表达量较高。同时陆封型香鱼的B一肌动蛋白、铁蛋白、氨基酰化酶、甲硫氨酸腺苷转移酶、过氧化物酶、丙氨酸乙醛酸转移酶和磷酸烯醇丙酮酸羧激酶则表达量较低。它们主要参与能量代谢、应激反应、氨基酸代谢等过程。由于wap65、HSP60和E13种蛋白在蛋白质组学结果中表达改变,且与应激和能量代谢有关,可能影响鱼类生长,因此采用荧光定量PCR（RT—PCR）验证陆封型和洄游型香鱼体肾wap65、HSP60和E1基因mR-NA表达差异,结果表明这3个基因mRNA表达均在陆封型香鱼体肾中较高,与蛋白质组学结果一致。综上,陆封型香鱼的几个糖酵解相关酶和应激蛋白表达量比洄游型香鱼高,而蛋白代谢相关酶表达量较低,揭示陆封型和洄游型香鱼在环境应激和能量代谢等层面有明显的差异。     

两种沼虾溶菌酶基因ORF的克隆和罗氏沼虾溶菌酶基因的组织表达(英文)

分别提取罗氏沼虾和日本沼虾血细胞总RNA,RT-PCR扩增获得特异性cDNA片段,纯化后克隆到T载体上。序列测定表明所克隆的两种沼虾溶菌酶基因的开放阅读框(ORF)为477bp,共编码158个氨基酸,包括溶菌酶成熟肽140个氨基酸残基和信号肽18个氨基酸残基。同源性分析表明,罗氏沼虾和日本沼虾溶菌酶基因的碱基序列及推测氨基酸序列高度同源,分别为99.4%和98.1%。两种沼虾溶菌酶基因的碱基序列和推测氨基酸序列与Gen-Bank上其他对虾溶菌酶的同源性达83.0%和80.0%以上。两种沼虾溶菌酶都具有c-型溶菌酶典型的两个酶活性位点(Glu51)和(Asp68),以及8个保守结构氨基酸残基Cys,且在101、106和107位上缺少Asp,因而推测本实验所克隆的两种沼虾溶菌酶基因属c-型溶菌酶基因的非钙结合亚型。以PCR法制备罗氏沼虾溶菌酶基因的生物素标记探针,斑点杂交检测感染弧菌后溶菌酶基因mRNA在各组织中的转录水平,结果表明受感染6h后在眼、肌肉、鳃、肝胰腺、肠管中的表达量均有升高,其中在肝胰腺中的表达量最高,约为对照组的560%。在不同感染时间里,肝胰腺中该基因表达量有较大的变化:感染后3h表达量最低,24h后表达量升至最高,大约为对照组的430%,48h时的表达量又有所下降,但仍明显高于对照组(约为330%)。受弧菌感染后罗氏沼虾溶菌酶基因转录的上调证明溶菌酶基因在非特异性免疫中的直接作用,同时表明肝胰腺可能在沼虾的免疫防御过程起重要作用。       

海参i型溶菌酶基因及其编码产物的结构特点

通过RT-PCR 和 RACE PCR技术,从海参(Stichopus japonicus)体壁中克隆得到一种溶菌酶基因(GenBank：EF036468).生物信息软件分析表明,其中全长cDNA为 713 bp,5′非编码区（UTR）246 bp,3′UTR 29 bp,开放阅读框438 bp,编码145个氨基酸,包括溶菌酶成熟肽124个氨基酸和信号肽21个氨基酸.对海参溶菌酶与多种无脊椎动物的c、g和i型溶菌酶进行分析比较,发现它与i型溶菌酶有较高的同源性,并具有i型溶菌酶高度保守的2个活性位点,即Glu34和Ser50.活性位点附近具有i型溶菌酶的一段特有的氨基酸保守序列MDVGSLSCG(P/Y)(Y/F)QIK,所以推断克隆的海参溶菌酶为i型.另外,通过搜索蛋白保守结构域数据库,发现海参溶菌酶与医用水蛭失稳酶相似性最高,并且这2个酶的三级结构模型也极其相似.因此推测,海参i型溶菌酶具有双功能特性,既能作用于细菌细胞壁的糖苷键使细胞裂解,又具有失稳酶的一些生化功能,能够水解纤维蛋白,这些特点在海参自溶过程中发挥重要的作用.     

日本鳗鲡肝脏表达抗菌肽2基因的克隆与表达

为探讨鱼类抗菌肽基因的生物学功能,研究应用RACE方法克隆获得了日本鳗鲡 (Anguilla japonica) 肝脏表达抗菌肽2基因 (Liver-Expressed Antimicrobial Peptide 2,LEAP-2),即AJLEAP-2的cDNA序列,全长为450 bp,开放阅读框编码89个氨基酸。其成熟肽含有LEAP-2保守基序C-X5-C-X4-C-X4-C。AJLEAP-2基因组结构与其他脊椎动物LEAP-2相同,都包含有三个外显子。利用荧光定量PCR检测了AJLEAP-2在日本鳗鲡不同组织/器官中的表达,发现其转录子在肝脏中表达量最高,是内参基因 (-actin) 的6倍; 其次是肠道,但其表达量仅为肝脏的1/130。此外,还检测了AJLEAP-2在日本鳗鲡玻璃鳗(Glass eel)阶段的转录表达水平,结果显示,玻璃鳗中AJLEAP-2的转录表达量仅低于黑仔期的肝脏,为黑仔鳗肠道表达量的2倍。LPS和迟缓爱德华菌 (Edwardsiella tarda) 刺激能显著上调鳗鲡血液中AJLEAP-2的转录表达,刺激16h后上调倍数最高,分别为对照组的86倍和12倍。此外,LPS刺激72h和E. tarda 刺激8h后,肠道中AJLEAP-2显著上调表达(P0.05),为对照组的8倍。Poly I:C刺激24h后,血液中AJLEAP-2转录表达显著下调。结果表明,AJLEAP-2在日本鳗鲡抗细菌感染过程中起重要的作用。     

日本鳗鲡IFN-γ基因的鉴定、表达模式及启动子活性分析

为揭示鱼类IFN-γ的生物学功能, 研究从日本鳗鲡(Anguilla japonica)中克隆获得了IFN-γ基因, 命名为AjIFN-γ。AjIFN-γ具有脊椎动物IFN-γ的典型特征: 包括4外显子/3内含子的基因结构、C端的IFN-γ特征性氨基酸基序和1个核定位信号, 以及6个α-螺旋反向平行构成的二级结构。AjIFN-γ在日本鳗鲡所有组织中均低水平转录表达, 其中肝脏中表达量最高, 其次是皮肤和头肾。Poly I:C刺激和迟缓爱德华氏菌感染均可显著诱导AjIFN-γ在鳃、头肾、体肾和(或)脾脏中的转录表达, 表明AjIFN-γ能够参与日本鳗鲡抗菌和抗病毒的免疫过程。此外, 研究还克隆了AjIFN-γ基因的5′调控区序列共1536 bp, 并构建了一系列Aj IFN-γ 5′调控区删节突变体, 分析其启动子活性, 结果表明, 上游–240/+136区域中含有起始AjIFN-γ转录的关键启动子调控元件, –1062/–814区域存在转录的正调控元件, 而–1252/–1062区域存在转录的负调控元件。上述结果进一步丰富了鱼类IFN-γ的基础知识。     

尼罗罗非鱼NITR基因的克隆鉴定与组织表达分析

从尼罗罗非鱼脾脏组织中克隆获得新型免疫受体(NITR,Novel immune-type receptor)基因的编码区序列(Gen Bank登录号:KX989509;命名为On-NITR),该基因c DNA全长1 119 bp,ORF为1 026 bp,可编码341个氨基酸,理论分子量为37.38k D,等电点为8.28。通过NCBI BLAST比对发现罗非鱼NITR与其他已报道的物种NITR氨基酸序列相似度为27%-46%。氨基酸序列分析显示:On-NITR具有1个信号肽区域、2个胞外Ig-domain区、1个跨膜结构域,以及1个胞质尾区,该胞质尾区含有NITR典型的免疫受体酪氨酸抑制基序(ITIM)和一个ITIM类似基序itim,且具有较高的保守性。荧光定量PCR分析显示,On-NITR在健康尼罗罗非鱼组织中均有表达,在肠道、皮肤、肝脏表达水平较高,在胸腺、鳃、脾脏、心脏、脑组织中的表达量较低,在头肾组织中的表达量最低。     

斑节对虾溶菌酶基因克隆及序列分析

参考对虾溶菌酶基因和类溶菌酶基因及其他多种生物的溶菌酶基因序列 ,设计并合成引物。运用RT PCR技术 ,从斑节对虾血细胞总RNA中扩增获得特异性片段。所获片段回收纯化后克隆到pGEM TEasyVector系统的T载体上。重组子的序列分析表明 ,所克隆的斑节对虾溶菌酶基因片段长 6 5 8bp ,包括溶菌酶基因开放阅读框 (ORF)4 77bp和 3′端非编码区的 181bp。 4 77bpORF共编码 15 8个氨基酸 ,包括溶菌酶成熟肽 14 0个氨基酸残基和信号肽 18个氨基酸残基。斑节对虾溶菌酶成熟肽推测分子量为 16 ,32kd ,等电点为 8 78。与南美白对虾溶菌酶基因的碱基序列及推测氨基酸序列比较 ,同源性分别为 89 5 %和 93 0 % ;与日本对虾类溶菌酶基因的同源性分别为 84 0 %和91 0 %。进一步的序列分析表明 ,斑节对虾溶菌酶氨基酸序列与多种类群生物的c 型溶菌酶氨基酸序列具有较高的同源性 ,并具有与c 型溶菌酶相同的活性位点氨基酸残基Glu51和Asp68,且与活性位点相邻的序列高度保守。斑节对虾溶菌酶氨基酸序列还具有与c 型溶菌酶相同的结构氨基酸——— 8个半胱氨酸残基。因而可认为所克隆的斑节对虾溶菌酶基因属c 型溶菌酶基因。     

日本鳗鲡TLR3基因的克隆及其免疫功能分析

Toll样受体3(TLR3)是用于识别双链RNA的一种重要模式识别受体。利用RT-PCR和RACE技术克隆了日本鳗鲡TLR3(Aj TLR3)基因c DNA全长序列,并采用实时荧光定量PCR(q RT-PCR)检测分析该基因在日本鳗鲡各组织器官以及体外肝脏细胞的表达水平变化,以期对日本鳗鲡TLR3基因的序列特征及其功能进行研究。结果表明:Aj TLR3基因全长3 383 bp,开放阅读框为2 766 bp,编码921个氨基酸。该蛋白具有16个LRR的胞外结构域、跨膜结构域以及TIR结构域,其中在TIR结构域含有一个高度保守的氨基酸残基Tyr~(778)。Aj TLR3基因在日本鳗鲡各组织器官中均有表达,其中肝脏表达量最高;经poly I∶C刺激后在血、肠、肝脏、脾脏、皮肤、心脏及肌肉组织中均显著提高;而LPS刺激后,仅在肝脏和肠中有显著提高。日本鳗鲡肝脏细胞体外实验结果显示:poly I∶C处理后12 h和24 h表达水平显著增高,Cp G-DNA和肽聚糖处理后24 h表达量均有显著增加;而细菌浓度达到107 CFU/m L和108 CFU/m L后,Aj TLR3基因表达水平分别在24 h、12 h显著增高并达到峰值。以上研究表明,Aj TLR3在日本鳗鲡抵御病毒及细菌的免疫应答过程中具有重要作用。     

Cloning and expression analysis of c-type and g-type lysozymes in yellow catfish (<Emphasis Type="Italic">Pelteobagrus fulvidraco</Emphasis>)

Lysozymes have important roles in innate immune system. Here, a c-type and a g-type lysozyme were identified from yellow catfish (Pelteobagrus fulvidraco). The deduced amino acid sequences of both lysozymes were conserved in catalytic sites and structural features as compared to their counterparts from other species. It was interesting that the g-type lysozyme possessed a signal peptide. The c-type and g-type lysozymes had the highest identity 89.4 and 76.2 % with that from channel catfish respectively. Phylogenetic analysis showed that the two lysozymes had a closely relationship with that from channel catfish and Astyanax mexicanus. Lysozymes from one order could form more than one clade in the phylogenetic tree, which indicated the gene duplications in evolution. Expression analysis with real time quantitative PCR revealed that the two lysozyme genes were constitutively expressed in all the tested tissues. The highest expression of c-type lysozyme was observed in liver, followed by spleen, head kidney, and trunk kidney, while the g-type lysozyme had highest expression in intestine, followed by spleen, head kidney, and trunk kidney. The mRNA levels of both genes were all up-regulated after challenging with Aeromonas hydrophila. However, there were differences in tissues and time points when the mRNA levels reached its peak between the two lysozymes. It indicated the diversity in regulation mechanisms and detailed functions among lysozymes. Taking together, these results will benefit the understanding of yellow catfish lysozymes.     

The primary structure of a novel goose-type lysozyme from rhea egg white

G-type lysozyme is a hydrolytic enzyme sharing a similar tertiary structure with plant chitinase. To discover the relation of function and structure, we analyzed the primary structure of new G-type lysozyme. The complete 185 amino acid residues of lysozyme from rhea egg white were sequenced using the peptides hydrolyzed by trypsin, V8 protease, and cyanogen bromide. Rhea lysozyme had sequence similarity to ostrich, cassowary, goose, and black swan, with 93%, 90%, 83%, and 82%, respectively. The six substituted positions were newly found at positions 3 (Asn), 9 (Ser), 43 (Arg), 114 (Ile), 127 (Met), and 129 (Arg) when compared with ostrich, cassowary, goose, and black swan lysozymes. The amino acid substitutions of rhea lysozyme at subsite B were the same as ostrich and cassowary lysozymes (Ser122 and Met123). This study was also constructed in a phylogenetic tree of G-type lysozyme that can be classified into at least three groups of this enzyme, namely, group 1; rhea, ostrich, and cassowary, group 2; goose, black swan, and chicken, and group 3; Japanese flounder. The amino acid sequences in assembled three alpha-helices found in this enzyme group (Thammasirirak, S., Torikata, T., Takami, K., Murata, K., and Araki, T., Biosci. Biotechnol. Biochem., 66, 147-156 (2002)) were also highly conserved, so that they were considered to be important for the formation of the hydrophobic core structure of the catalytic site and for maintaining a similar three-dimensional structure in this enzyme group.     

Evolution of cow nonstomach lysozyme genes.

Expansion of the lysozyme gene family is associated with the evolution of the ruminant lifestyle in ruminant artiodactyls such as the cow. Gene duplications allowed recombination between stomach lysozyme genes that may have assisted in the evolution of an enzyme adapted to survive and function in the stomach environment. Despite amplification of lysozyme genes, cow tears, milk, and blood are considered to be lysozyme deficient. Here we have identified 2 new cow lysozyme cDNA sequences and show that at least 4 different lysozymes are expressed in cows in nonstomach tissues and probably function as antibacterial defence enzymes. These 4 lysozyme genes are in addition to the 4 digestive lysozyme genes expressed in the stomach, yielding a number of expressed lysozyme genes in the cow larger than that found in most nonlysozyme-deficient mammals. In contrast to expectations, evidence for recombination between stomach and nonstomach lysozyme genes was found. Recombination, through concerted evolution, may have allowed some lysozymes to acquire the ability to survive in occasional acidic environments.     

Identification and expression analysis of three c-type lysozymes in Oreochromis aureus

Lysozyme is an important molecule of innate immune system for the defense against bacterial infections. Three genes encoding chicken-type (c-type) lysozymes, C1-, C2-, C3-type, were obtained from tilapia Oreochromis aureus by RT-PCR and the RACE method. Catalytic and other conserved structure residues required for functionality were identified. The amino acid sequence identities between C1- and C2-type, C1- and C3-type, C2- and C3-type were 67.8%, 65.7% and 63.9%, respectively. Phylogenetic tree analyze indicated the three genes were firstly grouped to those of higher teleosteans, Pleuronectiformes and Tetraodontiformes fishes, and then clustered to those of lower teleosteans, Cypriniformes fishes. Bioinformatic analysis of mature peptide showed that the three genes possess typical sequence characteristics, secondary and tertiary structure of c-type lysozymes. The three tilapia c-type lysozymes mRNAs were mainly expressed in liver and muscle, and C1-type lysozyme also highly expressed in intestine. C1-type lysozyme mRNA was weakly expressed in stomach, C2- and C3-type mRNAs were weakly expressed in intestine. After bacterial challenge, up-regulation was obvious in kidney and spleen for C1-type lysozyme mRNA, while for C2- and C3-type lysozyme obvious increase were observed in stomach and liver, suggesting that C1-type lysozyme may mainly play roles in defense, while C2- and C3-type lysozyme mainly conduct digestive function against bacteria infection. All the three c-type recombinant lysozymes displayed lytic activity against Gram-negative and Gram-positive bacteria. These results indicated that three c-type lysozymes play important roles in the defense of O. aureus against bacteria infections.     

Cloning of cDNAs and hybridization analysis of lysozymes from two oyster species, Crassostrea gigas and Ostrea edulis

In bivalve molluscs including oysters, lysozymes play an important role in the host defense mechanisms against invading microbes. However, it remains unclear in which sites/cells the lysozyme genes are expressed and which subsequently produced the enzyme. This study cloned lysozyme cDNAs from the digestive organs of Pacific oyster Crassostrea gigas and European flat oyster Ostrea edulis. Both complete sequences of two oysters' lysozymes were composed of 137 amino acids. Two translated proteins present a high content in cysteine residues. Phylogenetic analyses showed that these oysters' lysozymes clustered with the invertebrate-type lysozymes of other bivalve species. In the Pacific oyster, lysozyme mRNA was expressed in all tissues except for those of the adductor muscle. In situ hybridization analyses revealed that lysozyme mRNA was expressed strongly in basophil cells in the digestive gland tubule of C. gigas, but not in digestive cells. Results indicated that the basophil cells of the oyster digestive gland are the sites of lysozyme synthesis.     

Evolution of the bovine lysozyme gene family: Changes in gene expression and reversion of function

Recruitment of lysozyme to a digestive function in ruminant artiodactyls is associated with amplification of the gene. At least four of the approximately ten genes are expressed in the stomach, and several are expressed in nonstomach tissues. Characterization of additional lysozymelike sequences in the bovine genome has identified most, if not all, of the members of this gene family. There are at least six stomachlike lysozyme genes, two of which are pseudogenes. The stomach lysozyme pseudogenes show a pattern of concerted evolution similar to that of the functional stomach genes. At least four nonstomach lysozyme genes exist. The nonstomach lysozyme genes are not monophyletic. A gene encoding a tracheal lysozyme was isolated, and the stomach lysozyme of advanced ruminants was found to be more closely related to the tracheal lysozyme than to the stomach lysozyme of the camel or other nonstomach lysozyme genes of ruminants. The tracheal lysozyme shares with stomach lysozymes of advanced ruminants the deletion of amino acid 103, and several other adaptive sequence characteristics of stomach lysozymes. I suggest here that tracheal lysozyme has reverted from a functional stomach lysozyme. Tracheal lysozyme then represents a second instance of a change in lysozyme gene expression and function within ruminants. Correspondence to: D.M. Irwin     

Expression of lysozymes from Erwinia amylovora phages and Erwinia genomes and inhibition by a bacterial protein

Genes coding for lysozyme-inhibiting proteins (Ivy) were cloned from the chromosomes of the plant pathogens Erwinia amylovora and Erwinia pyrifoliae. The product interfered not only with activity of hen egg white lysozyme, but also with an enzyme from E. amylovora phage ΦEa1h. We have expressed lysozyme genes from the genomes of three Erwinia species in Escherichia coli. The lysozymes expressed from genes of the E. amylovora phages ΦEa104 and ΦEa116, Erwinia chromosomes and Arabidopsis thaliana were not affected by Ivy. The enzyme from bacteriophage ΦEa1h was fused at the N- or C-terminus to other peptides. Compared to the intact lysozyme, a His-tag reduced its lytic activity about 10-fold and larger fusion proteins abolished activity completely. Specific protease cleavage restored lysozyme activity of a GST-fusion. The bacteriophage-encoded lysozymes were more active than the enzymes from bacterial chromosomes. Viral lyz genes were inserted into a broad-host range vector, and transfer to E. amylovora inhibited cell growth. Inserted in the yeast Pichia pastoris, the ΦEa1h-lysozyme was secreted and also inhibited by Ivy. Here we describe expression of unrelated cloned 'silent' lyz genes from Erwinia chromosomes and a novel interference of bacterial Ivy proteins with a viral lysozyme.