大鲵Agouti基因的克隆、表达及多态性分析

刺鼠信号蛋白(Agouti)是哺乳动物和鸟类黑色素合成过程中的重要调控因子,影响动物的体色(毛色)。为研究Agouti在两栖动物体色形成过程中的作用,本研究利用PCR技术扩增得到大鲵Andrias davidianus的Agouti基因部分cDNA序列并进行了相关的生物信息学分析,进一步使用实时荧光定量PCR检测了大鲵Agouti基因在皮肤、肝脏等10个组织和器官中的表达情况,并检测了4种不同体色大鲵皮肤组织中Agouti基因的表达量。同时采用直接测序法,比较了不同体色大鲵Agouti基因编码区的序列差异。结果显示,大鲵Agouti基因cDNA序列长1 068 bp,开放阅读框399 bp,编码132个氨基酸残基。蛋白质同源性分析表明,大鲵Agouti蛋白具有与其他物种一致的保守Agouti结构域,其蛋白质序列与两栖爬行类序列相似性较高,与哺乳动物和鸟类相似性较低。系统进化分析显示,大鲵Agouti基因与高山倭蛙Nanorana parkeri、美国短吻鳄Alligator mississippiensis、中华鳖Pelodiscus sinensis等物种的亲缘关系较近。实时荧光定量PCR分析表明,Agouti基因mRNA在大鲵不同组织中均有表达,皮肤中的表达量最高。在4种不同体色大鲵皮肤组织中,黄色皮肤中的Agouti基因表达量高于其他体色。不同体色大鲵Agouti基因编码区序列一致。大鲵Agouti基因独特的序列特征及其表达的组织特异性暗示了其在两栖动物体色形成过程中可能具有与其他物种不同的调控机制。这些结果为进一步研究Agouti在大鲵体色形成过程中的作用提供了基础资料。     

小鼠Agouti基因变异及生物信息学分析

目的分析候选基因Agouti的多态性,揭示染色体工程小鼠毛色差异的分子机制。方法首先,用测色仪检测小鼠的毛色差异。其次,利用DNA芯片进行全基因组扫描确定候选基因Agouti。最后,运用生物信息学软件分析Agouti基因cDNA序列和氨基酸序列的多态性,预测突变对蛋白结构和功能产生的影响。结果发现Agouti基因cDNA序列上存在5个SNPs,使Agouti信号蛋白产生了3个错义突变。生物信息学分析发现,其中一个错义突变使该蛋白丢失了一个β折叠,并且其三级结构发生改变,最终导致与受体结合的能力相较于野生型有所下降。结论在毛色基因Agouti的编码区发现了一个新的错义突变,该突变使Agouti信号蛋白与受体结合能力下降,最终导致小鼠的毛色由浅灰色变为深灰色。     

小鼠Agouti基因和毛色表型相关问题及其遗传变异探究

目的对小鼠Agouti基因和毛色表型相关问题及其遗传变异情况进行分析探讨。方法抽取存在毛色差异的8个染色体工程小鼠作为研究对象,经电脑测色配色仪对品系、C3H/He小鼠毛色进行检测,并对检测结果进行统计分析。结果所抽取的8个品系K/S值分别处在C3H/He小鼠的K/S值两侧,按照C3H/He小鼠的K/S值划分界限,将抽取的8个品系小鼠划分成浅灰色、深灰色两个类型,DNA芯片分析发现,有一个鼠灰色相关基因Agouti,将Agouti基因作为候选基因,经Sanger法对候选基因c DNA序列进行检测。结果发现,Agouti基因开放读码框长396bp,编码131个氨基酸的Agouti信号蛋白。结论在候选基因Agouti编码区检测到突变(R96G)为重要错义突变,对α-MSH结合受体MC1R等能力进行了抑制,导致Agouti小鼠毛色偏向于黑色。     

绵羊黑色素合成相关基因的研究进展

毛色是一种可利用的遗传标记。在确定杂交组合、品种纯度和亲缘关系以及评价产品质量等方面均有一定的用途。哺乳动物毛色是由黑色素细胞产生的真黑素和褐黑素二者的分布和比例决定的。控制哺乳动物毛色色素的基因有很多,着重对黑色素合成相关基因酪氨酸酶基因(TYR)、黑素皮质激素受体1基因(MC1R)、鼠灰信号蛋白基因(Agouti)、酪氨酸酶相关蛋白1基因(TYRP1)的生物学功能及其遗传变异机制进行了综述。     

水通道蛋白的生理功能 ——水通道基因敲除小鼠表型研究进展

水通道蛋白 (aquaporin, AQP) 是一族细胞膜上选择性高效转运水分子的特异孔道. 自从 Agre 等于 1992 年从红细胞膜发现第一个水通道蛋白 AQP1以来,有关水通道蛋白结构与功能的研究取得了迅速的、系列性的进展 . 已报道的哺乳动物 AQP 家族已有 11 个在蛋白质序列上有同源性成员 (AQP0~AQP10). AQP 在体内各系统组织中广泛表达,除了在与体液分泌和吸收密切相关的多种上皮和内皮细胞高表达外,在一些与体液转运无明显关系的组织细胞如红细胞、白细胞、脂肪细胞和骨骼肌细胞等处也有表达,提示 AQP 可能在多种器官生理和病理中发挥重要作用. 基因打靶技术是研究特定基因在体内生理功能的有力手段. 目前 AQP1、3、4、5 基因敲除和 AQP2 基因点突变的基因敲入小鼠模型 ( 模拟人类常染色体隐性遗传尿崩症 ) 已成功建立并广泛用于表型研究,在 AQP 水通道蛋白生理功能方面获得许多重要进展.     

恒河猴PPARgamma基因的生物信息学分析

恒河猴 Macaca mulatta是继黑猩猩Pan troglodytes 后第2个完成基因组测序的非人类灵长类动物,在生命科学领域中具有重要意义.本文利用生物信息学方法寻找与人类肥胖密切相关的 PPARg 基因在恒河候中的同源基因,对该基因的序列、外显子信息、编码蛋白及其理化性质进行分析,并预测其编码蛋白的结构与功能,构建其同源基因的系统进化树,旨在为今后人类肥胖的相关研究提供一定的依据.     

肥胖与瘦蛋白抗性

瘦蛋白(leptin)是由肥胖的基因ob编码的一种多肽类激素,主要生理功能是调节能量代谢、抑制食欲,从而减少体重的增加。但是在人类和啮齿类动物中,均发现肥胖者中血浆瘦蛋白水平升高,所以推测肥胖者体内可能存在明显的瘦蛋白抗性(leptin resistance,LR)。     

人牛精浆蛋白相关新基因的cDNA克隆、定位和表达

为了研究牛精浆 (bovineseminalplasma ,BSP)蛋白及其相关蛋白在受精及受精卵发育中的重要作用 ,寻找BSP蛋白相关新基因 .采用cDNA末端快速扩增 (RACE)技术 ,克隆了一个BSP蛋白相关基因的cDNA序列 .应用辐射杂种细胞系 (RH)技术进行了基因染色体定位 .通过RT PCR检测了该基因在人体各组织中的表达情况 .并将该基因编码的蛋白进行了原核表达 .新基因的cDNA长度为 10 5 2bp ,其开放阅读框架 (ORF)编码了一个含 2 2 3个氨基酸残基的蛋白质 ,氨基酸序列中含有 4个纤连蛋白Ⅱ结构域 ,与BSP蛋白在结构上具有一定的相似性 ,称其为人BSP相关蛋白 (humanBSP relatedproteins ,HBRP) .该基因定位于染色体 19q13,在大肠杆菌中表达为 5 2kD的融合蛋白 .研究结果提示 ,应用RACE方法克隆了一种新的人类与BSP蛋白相关的基因 ,推测其编码蛋白是与BSP蛋白功能相关的结合蛋白 ,通过基因重组技术大量获得表达蛋白 ,对进一步研究新蛋白的生物学功能具有重要的意义 .     

SUMO与乳腺癌

小泛素修饰物(Small ubiquitin-like modifier,SUMO)是结构上与泛素类似的一种修饰蛋白,能与一些特定的靶蛋白共价连接.与泛素介导蛋白质的降解不同,SUMO化修饰调控主要对靶蛋白的功能,如在蛋白质的稳定性、细胞定位、信号转导、基因转录调控等方面均发挥着重要的作用.最近的研究表明:SUMO与乳腺癌的发生发展密切相关,它是通过SUMO化修饰参与并影响雌激素受体信号通路来实现的,本文将就此做一综述.     

微生物感染对瘦素影响的研究进展

瘦素是肥胖基因编码的一种蛋白产物,主要由白色脂肪组织产生。它在体内的主要生理功能是调节摄食和能量代谢,同时还参与多种神经－内分泌代谢系统的活动。感染是影响啮齿类动物瘦素分泌的重要因素之一,它可以影响血浆瘦素水平,从而参与影响机体的脂肪代谢;而内毒素和人类免疫缺陷病毒却并不影响人的血浆瘦素水平,但是幽门螺杆菌的感染可提高人胃基底部瘦素的表达。本文就还此作一简要回顾,并根据各类文献报道着重就感染对人和啮齿类动物血浆瘦素水平的影响作一描述。     

A new gene-finding tool: using the Caenorhabditis elegans operons for identifying functional partner proteins in human cells

How can a large number of different phenotypes be generated by a limited number of genotypes? Promiscuity between different, structurally related and/or unrelated proteins seems to provide a plausible explanation to this pertinent question. Strategies able to predict such functional interrelations between different proteins are important to restrict the number of putative candidate proteins, which can then be subjected to time-consuming functional tests. Here we describe the use of the operon structure of the nematode genome to identify partner proteins in human cells. In this work we focus on ion channels proteins, which build an interface between the cell and the outside world and are responsible for a growing number of diseases in humans. However, the proposed strategy for the partner protein quest is not restricted to this scientific area but can be adopted in virtually every field of human biology where protein-protein interactions are assumed.     

Virtual identification of essential proteins within the protein interaction network of yeast

Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organizational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has been observed to be correlated with its indispensability. Essential proteins generally have more interactions than the nonessential ones. We show here that the lethality associated with removal of a protein from the yeast proteome correlates with different centrality measures of the nodes in the PIN, such as the closeness of a protein to many other proteins, or the number of pairs of proteins which need a specific protein as an intermediary in their communications, or the participation of a protein in different protein clusters in the PIN. These measures are significantly better than random selection in identifying essential proteins in a PIN. Centrality measures based on graph spectral properties of the network, in particular the subgraph centrality, show the best performance in identifying essential proteins in the yeast PIN. Subgraph centrality gives important structural information about the role of individual proteins, and permits the selection of possible targets for rational drug discovery through the identification of essential proteins in the PIN.     

Deubiquitinating enzymes: their diversity and emerging roles

A growing number of important regulatory proteins within cells are modified by conjugation of ubiquitin, a well-conserved 76-amino-acid polypeptide. The ubiquitinated proteins are targeted to proteasome for degradation or alternative metabolic fates, such as triggering of plasma membrane endocytosis and trafficking to vacuoles or lysosomes. Deubiquitination, reversal of this modification, is being recognized as an important regulatory step. Deubiquitinating enzymes are cysteine proteases that specifically cleave off ubiquitin from ubiquitin-conjugated protein substrates as well as from its precursor proteins. Genome sequencing projects have identified more than 90 deubiquitinating enzymes, making them the largest family of enzymes in the ubiquitin system. This review will concentrate on recent important findings as well as new insights into the diversity and emerging roles of deubiquitinating enzymes in the ubiquitin-dependent pathway.     

Domains in proteins and proteoglycans of the extracellular matrix with functions in assembly and cellular activities

Most proteins of the extracellular matrix (ECM), such as the glycoproteins, collagens and proteoglycans, consist of many structurally autonomous domains that are often functionally distinct. Consequently these proteins are designated as mosaic proteins. Related domains are often found in several different ECM proteins. Domains which are of importance for assembly have been identified by fragmentation and other approaches. Triple-stranded coiled-coil domains in laminin and probably also in tenascin and thrombospondin are responsible for chain selection, a process which may be important for the formation of tissue specific isoforms. Globular domains at the C-terminus of collagenous domains are essential for the registration of the three chains and triple-helix formation. Fibrillar assemblies of these triple helices with constituent globular domains serve important assembly functions in many collagens including collagens IV and VI. Many other domains with more specialized functions in assembly have been identified in laminin, fibronectin and other ECM proteins. Cys-rich domains with either distant or close homology with epidermal growth factor are repeated manifold in rod-like regions of a number of ECM proteins including laminin, tenascin and thrombospondin. They may serve as spacer elements but as suggested for laminin some domains of this type may also function as signals for cellular growth and differentiation. Another important cellular function common to many ECM proteins is cell attachment. Several cell attachment sites have been localized in structurally unrelated domains of the same or of different ECM proteins.     

Advances in the production of membrane proteins in Pichia pastoris

Membrane proteins play key roles in diverse cellular functions and have become the target for a large number of pharmacological drugs. Despite representing about 20-30% of cellular proteins, their characterization is long overdue since they are difficult to handle, to purify from their natural source or to obtain as recombinant proteins. Pichia pastoris is a methylotrophic yeast species increasingly used as a host for heterologous protein expression for both research and industrial purposes. Over the past few years many efforts have allowed important advances in the development of this expression system for the expression and production of membrane proteins. The most recent achievements in improving yield and proper folding of integral membrane proteins are summarized in this review.     

Use of combinatorial peptide libraries for T-cell epitope mapping

T lymphocytes play important roles not only in infectious diseases and autoimmunity, but also in immune responses against tumors. For many of these disorders, the relevant target antigens are not known. Designing effective methods that allow the search for T-cell epitopes is therefore an important goal in the areas of infectious diseases, oncology, vaccine development, and numerous other biomedical specialties. So far, the strategies used to examine T-cell recognition have been based largely on mapping T-cell epitopes with overlapping peptides from known proteins or with entire proteins, e.g., from a specific virus, bacterium, or human tissue. These approaches are tedious and have a number of limitations. It is, for example, almost impossible to isolate T cells that infiltrate an organ or infectious site and identify their specificity unless one already has a concept as to which antigens may be relevant. During recent years, a number of laboratories have developed less biased approaches that employ either the selection of putative T-cell epitopes based on the prediction of binding to certain major histocompatibilty complex (MHC) molecules and peptide or protein libraries that have been generated in expression systems, e.g. phage, or rely on combinatorial peptide chemistry. The latter technique has been refined by a number of laboratories including ours. Bead-bound or, preferably, positional scanning synthetic and soluble combinatorial peptide libraries allow the identification of T-cell epitopes within complex mixtures of proteins even for T cells that have been expanded from an organ infiltrate with a polyclonal stimulus. The practical steps that are involved in the latter method are described in this article.     

Protein evolution is faster outside the cell

Some proteins are highly conserved across all species, whereas others diverge significantly even between closely related species. Attempts have been made to correlate the rate of protein evolution to amino acid composition, protein dispensability, and the number of protein-protein interactions, but in all cases, conflicting studies have shown that the theories are hard to confirm experimentally. The only correlation that is undisputed so far is that highly/broadly expressed proteins seem to evolve at a lower rate. Consequently, it has been suggested that correlations between evolution rate and factors like protein dispensability or the number of protein-protein interactions could be just secondary effects due to differences in expression. The purpose of this study was to analyze mammalian proteins/genes with known subcellular location for variations in evolution rates. We show that proteins that are exported (extracellular proteins) evolve faster than proteins that reside inside the cell (intracellular proteins). We find weak, but significant, correlations between evolution rates and expression levels, percentage of tissues in which the proteins are expressed (expression broadness), and the number of protein interaction partners. More important, we show that the observed difference in evolution rate between extra- and intracellular proteins is largely independent of expression levels, expression broadness, and the number of protein-protein interactions. We also find that the difference is not caused by an overrepresentation of immunological proteins or disulfide bridge-containing proteins among the extracellular data set. We conclude that the subcellular location of a mammalian protein has a larger effect on its evolution rate than any of the other factors studied in this paper, including expression levels/patterns. We observe a difference in evolution rates between extracellular and intracellular proteins for a yeast data set as well and again show that it is completely independent of expression levels.     

A technically detailed and pragmatic protocol for quantitative serum proteomics using iTRAQ

Blood is recognised as a highly important source of disease-related biomarkers, and proteomic approaches for identifying novel blood-borne biomarkers are in demand. The complexity and dynamic protein concentration range of plasma/serum however complicates the analysis process. A number of strategies for simplification of blood prior to proteomic analysis have been developed. In addition, methods for quantifying the levels of proteins in samples, such as isobaric tags for relative and absolute quantification (iTRAQ) are emerging. However, the successful application of these procedures is not always straightforward and technical hurdles must be overcome. Here we provide a technically detailed working protocol for iTRAQ-based quantification of serum proteins following immunodepletion of high abundance proteins. To improve the number of proteins identified and quantified we have introduced several modifications to the standard iTRAQ protocol. We report identifications of 217 proteins (5773 peptides) with a false discovery rate of 1% or 254 proteins with 95% confidence, respectively. Relative quantification data were obtained for 234 (95% confidence) serum proteins, including species present in the concentration range of tissue leakage factors. The samples described here relate to pancreatic cancer; however the protocol can be applied to serum from other control or disease types.     

Mapping the binding sites of challenging drug targets

An increasing number of medically important proteins are challenging drug targets because their binding sites are too shallow or too polar, are cryptic and thus not detectable without a bound ligand or located in a protein–protein interface. While such proteins may not bind druglike small molecules with sufficiently high affinity, they are frequently druggable using novel therapeutic modalities. The need for such modalities can be determined by experimental or computational fragment based methods. Computational mapping by mixed solvent molecular dynamics simulations or the FTMap server can be used to determine binding hot spots. The strength and location of the hot spots provide very useful information for selecting potentially successful approaches to drug discovery.