Characterization of two genes encoding leucine-rich repeat-containing proteins in grass carp Ctenopharyngodon idellus

The cDNAs and genes of two different types of leucine- rich repeat-containing proteins from grass carp ( Ctenopharyngodon idellus) were cloned. Homology search revealed that the two genes, designated as GC-GARP and GC-LRG, have 37% and 32% deduced aminoacid sequence similarities with human glycoprotein A repetitions predominant precursor ( GARP) and leucine-rich alpha2-glycoprotein (LRG), respectively. The cDNAs of GC-GARP and GC-LRG encoded 664 and 339 amino acid residues, respectively. GC-GARP and GC-LRG contain many distinct structural and/or functional motifs of the leucine- rich repeat (LRR) subfamily, such as multiple conserved 11-residue segments with the consensus sequence LxxLxLxxN/CxL ( x can be any amino acid). The genes GC-GARP and GC-LRG consist of two exons, with 4,782 bp and 2,119 bp in total length, respectively. The first exon of each gene contains a small 5'-untranslated region and partial open reading frame. The putative promoter region of GC-GARP was found to contain transcription factor binding sites for GATA-1, IRF4, Oct-1, IRF-7, IRF-1, AP1, GATA-box and NFAT, and the promoter region of GC-LRG for MYC-MAX, MEIS1, ISRE, IK3, HOXA9 and C/EBP alpha. Phylogenetic analysis showed that GC-GARP and mammalian GARPs were clustered into one branch, while GC-LRG and mammalian LRGs were in another branch. The GC-GARP gene was only detected in head kidney, and GC-LRG in the liver, spleen and heart in the copepod ( Sinergasilus major)- infected grass carp, indicating the induction of gene expression by the parasite infection. The results obtained in the present study provide insight into the structure of fish LRR genes, and further study should be carried out to understand the importance of LRR proteins in host - pathogen interactions.

Utilization of several plant proteins by gibel carp (Carassius auratus gibelio)

Six isonitrogenous (gross protein content 35%) and isoenergetic (gross energy content 17 kJ g(-1)) diets were formulated to investigate the effects of inclusion of plant proteins on the gibel carp (Carassius auratus gibelio L.). The plant proteins tested were: soybean cake (SBC), potato protein concentrate (PPC), peanut cake (PNC), cottonseed cake (CSC) and rapeseed cake (RSC). Fish meal (FM) was used as control. In each diet, 27% of the protein was supplied by fish meal, and the rest supplied by the plant protein tested. Each diet was fed to three groups of gibel carp for 8 weeks in a recirculation system. Specific growth rate (SGR) in fish fed the control diet was significantly higher than those in the other groups, and SGR in fish fed the PPC was significantly lower than in fish fed other plant proteins. There was no significant difference in SGR among the other groups. Feeding rates were ranked in the order: RSC > CSC > FM > PNC > SBC > PPC. Conversion efficiency was highest in groups fed FM, SBC and PNC, followed by groups fed CSC and RSC, and was lowest in the group fed PPC. The fish fed PPC showed lower protein retention than those fed FM and SBC. FM showed highest energy retention while PPC showed lowest, There was no significant relationship between SGR and intake of digestible protein (g g(-1) day(-1)), digestible lysine (g g(-1) day(-1)), digestible methionine (g g(-1) day(-1)) or digestible total essential amino acids (g g(-1) day(-1)), suggesting that the differences in SGR could not alone account for any of these variables.

Ras 超家族蛋白的起源演化研究

Ras 超家族蛋白是真核生物中普遍存在的一类小分子GTP 结合蛋白。它们 具有高度保守的GTP 结合结构域，根据序列结构和细胞功能被分为七个家族： Sar1、Arf、SRβ、Ran、Rab、Rho 和Ras。这些蛋白分别行使着真核生物特有的 细胞功能，诸如运输小泡的形成和转运（Sar1、Arf、Rab），胞质骨架的建成（Rho）， 细胞核-胞质运输及核膜重建（Ran）等，其起源演化和真核细胞的起源密切相关。 本文利用生物信息学手段和分子生物学实验调查研究了原核生物和原生生物中 Ras 超家族蛋白同源物的存在情况，并进行了分子系统分析，对Ras 超家族蛋白 的起源演化问题进行了较为深入、系统的探讨。获得了以下结果和结论： 1）通过原核生物基因组的搜索和序列结构分析，在一些真细菌中首次鉴定 出了高度相似于真核生物Ras 超家族蛋白的原核生物同源物，且实验证明它们的 基因具有表达活性；在原细菌中的产甲烷菌和热原体中也发现有序列分歧较大的 同源物。并在更多的真细菌种类中鉴定出了更多的前人已报道的另一种小分子 GTP 结合蛋白—MglA。序列比对分析表明MglA 蛋白具有自己独特的序列特征， 与真核生物的Ras 超家族蛋白序列差异较大。进一步的分子系统分析显示：真核 生物Ras 超家族蛋白的七个家族中，Ran、Rab、Rho 和Ras 等四个家族聚在一 起，上述我们所鉴定的真细菌的Ras 超家族蛋白同源物则紧聚在其外围；真核生 物的另三个家族（Sar1、Arf、SRβ）聚成另一枝，并接着与产甲烷原细菌的的同 源物及真细菌的MglA 蛋白聚在一起。这些结果表明：Ras 超家族蛋白不是前人 所认为的为真核生物所特有，实际上在一些原核生物中就已产生；真核生物Ras 超家族蛋白的祖先也不太可能是前人所认为的为真细菌的MglA；真核生物Ras 超家族蛋白的七个家族可能有两种不同的起源：Ran、Rab、Rho 和Ras 等可能 来源于蓝细菌或蛋白菌，或二者的共同祖先，而Sar1、Arf 和SRβ 可能来源于产 甲烷原细菌，这也可能反映了真核细胞“融合起源”的历史。 2）通过搜索一些较为低等的单细胞真核生物——原生生物基因组中Ras 超 家族蛋白，并结合一系列其他处在不同进化地位真核生物的Ras 超家族蛋白进行 分析，发现Sar1、Arf、Rab 和Ran 家族的蛋白在真核生物中普遍存在，而SRβ、 Rho 和Ras 家族蛋白在有些真核生物中未找到。根据各家族蛋白在真核生物中的分布情况推测在真核生物的最近共同祖先中存在的Ras 超家族蛋白可能有下列 两种情况：（1）最近的共同祖先已经具有了所有七个家族的蛋白，并且至少有 11 个成员：1 个Sar1、1 个SRβ、3 个Arf（Arf1、Arl1、Arl2）、3 个Rab（Rab1、 Rab6、Rab11）、1 个Ran、1 个Rho（Rac）和1 个Ras（RheB）。因而，部分真 核生物中缺少SRβ、Rho 和Ras 家族蛋白很可能是因基因丢失所致。植物中Ras 家族蛋白的缺少应该是由于在进化早期，其祖先绿藻丢失了单个Ras 家族蛋白基 因所致；（2）根据Cavalier-Smith 的真核生物划分为单鞭毛（变形虫类、真菌和 后生动物）和双鞭毛（藻类、植物和除变形虫外的原生动物）两大类的分类观点， 真核生物最近的共同祖先可能只具有除Ras 家族而外的六个家族的成员，而Ras 家族蛋白则是在此两大类群分化以后在单鞭毛类生物中才产生的，多数双鞭毛类 生物如原生动物、绿藻和植物中没有Ras 的情况应该是一种祖征，而个别双鞭毛 类生物如红藻具有的Ras 家族蛋白则很可能是从单鞭毛类生物那里水平基因转 移而来的。至于SRβ 和Rho 家族蛋白在部分物种中的缺少，则还是可能因为基 因丢失所致。此外，变形虫类生物中大量的Ras 超家族蛋白提示基因组的大小或 进化地位的高低并不是Ras 超家族蛋白成员多少的决定性因素，而细胞相应生理 活动的需求才是家族成员增多的关键。

Pressurized electrochromatography coupled with electrospray ionization mass spectrometry for analysis of peptides and proteins

Pressurized capillary electrochromatography (pCEC) was coupled with electrospray ionization mass spectrometry (ESI-MS) using a coaxial sheath liquid interface. It was used for separation and analysis of peptides and proteins. The effects of organic modifier and applied voltage on separation were investigated, and the effects of pH value of the mobile phase and the concentration of the electrolyte on ESI-MS signal were investigated. The resolution and detection sensitivity with different separation methods (pCEC, capillary high-performance liquid chromatography) coupled on-line with mass spectrometry were compared for the separation of a peptide mixture. To evaluate the feasibility and reliability of the experimental setup of the system, tryptic digests of cytochrome c and modified protein as real samples were analyzed by using pCEC-ESI-MS.

Detection of K-ras exon 1 mutations by constant denaturant capillary electrophoresis

Among various mutation detection methods, constant denaturant capillary electrophoresis (CDCE) is one of the most common techniques for rapid identification of known or unknown mutations. In this report, a CDCE analysis method with homemade linear polyacrylamide (LPA) kit was developed on ABI 310 genetic analyzer, the effect and relationship of various denaturing factors in CDCE analysis were investigated and K-ras gene mutations of 31 coloerctal cancer patients were detected. Results indicate that, with the increase of chemical danaturant concentration, the optimum temperature was lowered, and when the concentration of urea (formamide) was higher than 7 M (40%), the homoduplex and heteroduplex of mutant samples were separated with difficulty. Detection results of K-ras gene in colorectal samples indicated that mutations were present in eight (26%) of 31 patients; most mutations were localized in codon 12, which is thought to be a critical step and plays an important role in human colorectal carcinogenesisas. Copyright (C) 2004 John Wiley Sons, Ltd.

Simultaneous genotyping of multiplex single nucleotide polymorphisms of the K-ras gene with a home-made kit

Accurate and fast genotyping of single nucleotide polymorphisms (SNPs) is important in the human genome project. Here an automated fluorescent method that can rapidly and accurately genotype multiplex known SNPs was developed by using a homemade kit, which has lower cost but higher resolution than commercial kit. With this method, oncogene K-ras was investigated, four known SNPs of K-ras gene exon 1 in 31 coloerctal cancer patients were detected. Results indicate that mutations were present in 8(26%) of 31 patients, and most mutations were localized in codon 12. The presence of these mutations is thought to be a critical step and plays an important role in human colorectal carcinogenesisas. (C) 2003 Elsevier B.V. All rights reserved.

Immobilized metal-ion chelating capillary microreactor for peptide mapping analysis of proteins by matrix assisted laser desorption/ionization-time of flight-mass spectrometry

Peptide mass mapping analysis, utilizing a regenerable enzyme microreactor with metal-ion chelated adsorption of enzyme, combined with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was developed. Different procedures from the conventional approaches were adopted to immobilize the chelator onto the silica supports, that is, the metal chelating agent of iminodiacetic acid (IDA) was reacted with glycidoxypropyltrimethoxysilane (GLYMO) before its immobilization onto the inner wall of the fused-silica capillary pretreated with NH4HF2. The metal ion of copper and subsequently enzyme was specifically adsorbed onto the surface to form the immobilized enzyme capillary microreactor, which was combined with MALDI-TOF-MS to apply for the mass mapping analysis of nL amounts of protein samples. The results revealed that the peptide mapping could routinely be generated from 0.5 pmol protein sample in 15 min at 50degreesC, even 20 fmol cytochrome c could be well digested and detected.

Affinity membrane chromatography for the analysis and purification of proteins

Affinity chromatography is unique among separation methods as it is the only technique that permits the purification of proteins based on biological functions rather than individual physical or chemical properties. The high specificity of affinity chromatography is due to the strong interaction between the ligand and the proteins of interest. Membrane separation allows the processing of a large amount of sample in a relatively short time owing to its structure, which provides a system with rapid reaction kinetics. The integration of membrane and affinity chromatography provides a number of advantages over traditional affinity chromatography with porous-bead packed columns, especially with regard to time and recovery of activity. This review gives detailed descriptions of materials used as membrane substrates, preparation of basic membranes, coupling of affinity ligands to membrane supports, and categories of affinity membrane cartridges. It also summarizes the applications of cellulose/glycidyl methacrylate composite membranes for proteins separation developed in our laboratory. (C) 2001 Elsevier Science B.V. All rights reserved.

Quantitative electrochemiluminescence detection of proteins: Avidin-based sensor and tris(2,2 '-bipyridine) ruthenium(II) label

Quantitative electrochemilumineseence (ECL) detection of a model protein, bovine serum albumin (BSA) was achieved via biotin-avidin interaction using an avidin-based sensor and a well-developed ECL system of tris(2,2'-bipyridine) ruthenium(II) derivative as label and tri-n-propylamine (TPA) as coreactant. To detect the protein, avidin was linked to the glassy carbon electrode through passive adsorptions and covalent interaction with carboxylate-terminated carbon nanotubes that was used as binder to immobilize avidin onto the electrode. Then, biotinylated BSA tagged with tris(2,2'-bipyridine) ruthenium(II) label was attached to the prepared avidin surface.

Microchip Micellar Electrokinetic Chromatography Based on One Functionalized Ionic Liquid and Its Excellent Performance on Proteins Separation

Herein, one water-soluble functionalized ionic liquid (IL), 1-butyl-3-methylimidazolium dodecanesulfonate (BAS), was designed, investigated and successfully applied to microchip micellar electrokinetic chromatography (MEKC) construction. It possessed the properties of both IL and surfactant. A fairly stable pH value similar to 7.4, which was fit to pH values of general biological buffers, was nicely placed at the optimum concentration of 20 mM BAS solution. While applying BAS solution as running buffer in poly(dimethylsiloxane) (PDMS) microfluidic systems, significantly enhanced electroosmotic flow (8-fold) and resolutions between analytes were obtained than that using other supporting electrolytes or surfactants.

The immobilization of proteins on biodegradable polymer fibers via click chemistry

A facile and efficient method to immobilize bioactive proteins onto polymeric substrate was established. Testis-specific protease 50 (TSP50) was immobilized on ultrafine biodegradable polymer fibers, i.e., (1) to prepare a propargyl-containing polymer P(LA90-co-MPCIO) by introducing propargyl group into a cyclic carbonate monomer (5-methyl-5-propargyloxycarbonyl-1,3-dioxan2-one, MPC) and copolymerizing it with L-lactide; (2) to electrospin the functionalized polymer into ultrafine fibers; (3) to azidize the TSP50, and (4) to perform the click reaction between the propargyl groups on the fibers and the azido groups on the protein.

A New Method for Analysis of Disulfide-Containing Proteins by Matrix-Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry

A simple and high-throughput method for the identification of disulfide-containing peptides utilizing peptide-matrix adducts is described. Some commonly used matrices in MALDI mass spectrometry were found to specifically react with sulfhydryl groups within peptide, thus allowing the observation of the peptide-matrix adduct ion [M + n + n' matrix + H](+) or [M + n + n' matrix + Na](+) (n = the number of cysteine residues, n' = 1, 2, ..., n) in MALDI mass spectra after chemical reduction of disulfide-linked peptides. Among several matrices tested, alpha-cyano-4-hydroxycinnamic acid (CHCA, molecular mass 189 Da) and alpha-cyano-3-hydroxycinnamic acid (3-HCCA) were found to be more effective for MALDI analysis of disulfide-containing peptides/proteins. Two reduced cysteines involved in a disulfide bridge resulted in a mass shift of 189 Da per cysteine, so the number of disulfide bonds could then be determined, while for the other matrices (sinapinic acid, ferulic acid, and caffeic acid), a similar addition reaction could not occur unless the reaction was carried out under alkaline conditions. The underlying mechanism of the reaction of the matrix addition at sulfhydryl groups is proposed, and several factors that might affect the formation of the peptide-matrix adducts were investigated.