我国汉族人载脂蛋白AI/CIII基因的分子克隆和初步结构分析

脂蛋白代谢异常和动脉粥样硬化及冠心病的发病有密切关系,而载脂蛋白在人体脂蛋白代谢中起重要作用。近年来,国外对载脂蛋白基因的分子生物学研究取得了众多成就,已从基因文库克隆了各种载脂蛋白基因,对它们结构和功能的关系进行了深入研究;并且发现,     

植物功能性状、功能多样性与生态系统功能: 进展与展望

植物功能性状与生态系统功能是生态学研究的一个重要领域和热点问题。开展植物功能性状与生态系统功能的研究不仅有助于人类更好地应对全球变化情景下生物多样性丧失的生态学后果,而且能为生态恢复实践提供理论基础。近二十年来,该领域的研究迅速发展,并取得了一系列的重要研究成果,增强了人们对植物功能性状-生态系统功能关系的认识和理解。本文首先明确了植物功能性状的概念, 评述了近年来植物功能性状-生态系统功能关系领域的重要研究结果, 尤其是植物功能性状多样性-生态系统功能关系研究现状; 提出了未来植物功能性状与生态系统功能关系研究中应加强植物地上和地下性状之间关系及其与生态系统功能、植物功能性状与生态系统多功能性、不同时空尺度上植物功能性状与生态系统功能, 以及全球变化和消费者的影响等方面。     

褪黑素与植物抗逆性研究进展

褪黑素广泛存在于植物体内,对植物生长和发育方面有着重要的作用。其中,最为人们关注的是褪黑素在植物抵御干旱、高盐、极端温度和氧化胁迫等不良影响中所发挥的重要功能。随着人们对褪黑素研究的深入,褪黑素在植物体中发挥的作用和功能也更加明确,国内外在褪黑素与植物抗逆性关系的研究也取得了丰硕的成果。主要从植物体中褪黑素的合成途径、褪黑素在植物抗性反应中的作用以及内源褪黑素含量与逆境等方面进行了综述,并提出今后的研究方向。可以归纳为:植物体内褪黑素的合成机制与动物体内相似,但是确切的生物合成途径和具体的合成位点尚未明确;外源褪黑素处理能够增强植物抵御逆境的能力;逆境胁迫能够促进植物自身合成褪黑素,过表达褪黑素合成相关基因能够增加植物体内褪黑素的含量。     

组蛋白去乙酰化酶(HDACs)及其在植物中的作用

组蛋白去乙酰化酶(HDACs)是一个在真核生物(包括酵母、哺乳动物和植物)中广泛存在的超基因家族。HDACs与组蛋白乙酰基转移酶(HATs)共同作用来调节组蛋白乙酰化的状态,从而影响染色体的结构和功能,调节基因的转录和细胞的多种功能。目前,人们对植物HDACs的研究逐渐增多,很多HDAC基因在不同植物中得到鉴定和研究。综述了HDACs的分类以及在植物生长发育和胁迫反应中的作用,旨在为进一步研究HDAC在植物中的表观遗传调控机理以及培育抗逆新品种奠定理论基础。     

植物科学画在植物科学研究发展中的重要性

植物科学画是一门专业技术性较强的学科,所描绘出的画面内容,是艺术性与科学性的有机结晶。植物科学绘画以其特殊的应用和辅助功能,能科学、客观、真实、艺术地表达植物科学内容。随着人们对植物科学研究的不断深入和发展,植物科学画已经形成了独特的、直观性的艺术语言表达方式,在世界各国不同时期编著的各类植物学研究志书、专著、期刊和杂志中,植物科学绘画具有了举足轻重的地位。该文对植物科学绘画的特性进行了研究,并分析其科学性与艺术性的内涵; 阐述了植物科学画在欧洲各国和中国本草药学时期和植物分类学研究时期的发展与应用。研究表明植物科学画在植物科学研究发展过程中发挥了重要作用。     

用于基因组分析的模式植物拟南芥

长期以来,人们对植物结构和功能的认识,都是建立在对大量物种的研究,特别是对那些与农业相关物种的深入研究上。尽管已获得了大量信息,但对植物的开花、根的生长、激素运动以及植物对环境信号的反应等方面的认识仍很有限。为此,人们在深入研究植物的生长与发育时,曾经将玉米、番茄、豌豆、水稻、大麦、矮牵牛和金鱼草等植物作为模式模式基因系统来研究,但其结果都不尽人意。直至人们找到了拟南芥这种模式植物以后,才在广大的生物学家中达成共识。拟南芥（Ａｒａｂｉｄｏｐｓｉｓｔｈａｌｉａｎａ）是十字花科一年生草本植物,高１５…     

陆地生态系统植物功能群研究进展

从植物功能群角度探讨陆地生态系统功能与稳定性维持机理、植物对环境变化的适应与响应以及水分、养分利用效率等成为当前生态系统生态学研究的主要技术路线.植物功能群的提出和研究,为研究复杂的生态系统提供了一个良好的方法和途径.综述了陆地生态系统功能群方面的最新研究进展,介绍了植物功能群定义的发展历程,详细比较了植物功能群划分的依据及方法,对于植物功能群与群落稳定性之间的关系、植物功能群对群落生产力的影响以及植物功能群与环境因子的动态关系等进行了深入讨论.这些研究资料表明,植物功能群整合了功能及对环境响应相似的一类植物,但植物功能特征不是绝对的、单一的,所以对植物功能群就会有不同的理解,会有不同的定义及划分方法.许多研究者从不同的角度、尺度来对植物功能群进行研究,这些研究结果有不同的针对方向和目的,使人们可以从不同的角度更全面的理解复杂的陆地生态系统.学者们在研究生态系统时,或多或少地总要与植物功能群相联系,这大大拓宽了植物功能群的应用范围.所有前人的研究使植物功能群的概念、划分、方向、应用等诸方面越来越清晰.这要求应有一个规范、统一、明确的植物功能群研究方案,这样能使对植物功能群的研究更加深入,能整合全球所有植物功能群的相关研究.     

植物根构型的定量分析

植物根系具有锚定植株、吸收和运输土壤中的水分及养分、合成和贮藏营养物质等重要功能。根构型是根系在土壤中的空间造型和分布。对植物根构型进行定量分析, 有助于人们了解根系结构和根系功能在生态系统中的重要作用。本文对植物根构型的概念及其定量分析研究进展进行了概述, 并介绍了植物根构型的主要研究方法和定量分析技术。     

植物根构型的定量分析

植物根系具有锚定植株、吸收和运输土壤中的水分及养分、合成和贮藏营养物质等重要功能。根构型是根系在土壤中的空间造型和分布。对植物根构型进行定量分析,有助于人们了解根系结构和根系功能在生态系统中的重要作用。本文对植物根构型的概念及其定量分析研究进展进行了概述,并介绍了植物根构型的主要研究方法和定量分析技术。     

宏观生态学中的植物功能性状研究:历史与发展趋势

植物功能性状通常是指能直接或间接影响植物生长、存活和繁殖的形态学、生理学和物候学等相对稳定和可测量的特征参数。经过多年发展,植物功能性状的定义、内涵以及测量手段已经科学化和规范化,人们利用在不同地点、不同时间测定的数据,深入阐述了植物功能性状的种内与种间变异、区域乃至全球植物功能性状的空间变异规律及其调控机制、多种功能性状间的协同与权衡以及植物功能性状的演化等。随着20世纪90年代开始的大尺度和全球整合型植物功能性状数据库的逐步建成,植物功能性状的研究已经不再局限于个体、特定群落和局域尺度:一方面,区域和全球的植物功能性状生物地理学研究蓬勃发展;另一方面,植物功能性状研究也逐步被拓展到群落物种共存机制、生态系统功能形成与变异等的机理解释。随着植物功能性状研究逐步深入到复杂的自然群落或生态系统,科研人员发现传统“零星数据收集性数据库”难以很好地满足相关数据要求,迫切需要考虑与群落复杂性和植物不同器官功能性状相匹配的新型数据库,该数据库的基本要求和特色是基于原位群落调查和多种功能性状协同测量。随着科学概念和新型数据库的发展,相关研究呈现出如下发展趋势:1)进一步强调了植物不同器官间功能性状...     

Identification, expression, and evolutionary analyses of plant lipocalins

Lipocalins are a group of proteins that have been characterized in bacteria, invertebrate, and vertebrate animals. However, very little is known about plant lipocalins. We have previously reported the cloning of the first true plant lipocalins. Here we report the identification and characterization of plant lipocalins and lipocalin-like proteins using an integrated approach of data mining, expression studies, cellular localization, and phylogenetic analyses. Plant lipocalins can be classified into two groups, temperature-induced lipocalins (TILs) and chloroplastic lipocalins (CHLs). In addition, violaxanthin de-epoxidases (VDEs) and zeaxanthin epoxidases (ZEPs) can be classified as lipocalin-like proteins. CHLs, VDEs, and ZEPs possess transit peptides that target them to the chloroplast. On the other hand, TILs do not show any targeting peptide, but localization studies revealed that the proteins are found at the plasma membrane. Expression analyses by quantitative real-time PCR showed that expression of the wheat (Triticum aestivum) lipocalins and lipocalin-like proteins is associated with abiotic stress response and is correlated with the plant's capacity to develop freezing tolerance. In support of this correlation, data mining revealed that lipocalins are present in the desiccation-tolerant red algae Porphyra yezoensis and the cryotolerant marine yeast Debaryomyces hansenii, suggesting a possible association with stress-tolerant organisms. Considering the plant lipocalin properties, tissue specificity, response to temperature stress, and their association with chloroplasts and plasma membranes of green leaves, we hypothesize a protective function of the photosynthetic system against temperature stress. Phylogenetic analyses suggest that TIL lipocalin members in higher plants were probably inherited from a bacterial gene present in a primitive unicellular eukaryote. On the other hand, CHLs, VDEs, and ZEPs may have evolved from a cyanobacterial ancestral gene after the formation of the cyanobacterial endosymbiont from which the chloroplast originated.     

A phylogenetic analysis of the lipocalin protein family

The lipocalins are a family of extracellular proteins that bind and transport small hydrophobic molecules. They are found in eubacteria and a great variety of eukaryotic cells, in which they play diverse physiological roles. We report here the detection of two new eukaryotic lipocalins and a phylogenetic analysis of 113 lipocalin family members performed with maximum-likelihood and parsimony methods on their amino acid sequences. Lipocalins segregate into 13 monophyletic clades, some of which are grouped in well-supported superclades. An examination of the G + C content of the bacterial lipocalin genes and the detection of four new conceptual lipocalins in other eubacterial species argue against a recent horizontal transfer as the origin of prokaryotic lipocalins. Therefore, we rooted our lipocalin tree using the clade containing the prokaryotic lipocalins. The topology of the rooted lipocalin tree is in general agreement with the currently accepted view of the organismal phylogeny of arthropods and chordates. The rooted tree allows us to assign polarity to character changes and suggests a plausible scenario for the evolution of important lipocalin properties. More recently evolved lipocalins tend to (1) show greater rates of amino acid substitutions, (2) have more flexible protein structures, (3) bind smaller hydrophobic ligands, and (4) increase the efficiency of their ligand-binding contacts. Finally, we found that the family of fatty-acid-binding proteins originated from the more derived lipocalins and therefore cannot be considered a sister group of the lipocalin family.     

Evolution of the lipocalin family as inferred from a protein sequence phylogeny

The lipocalins constitute a family of proteins that have been found in eubacteria and a variety of eukaryotic cells, where they play diverse physiological roles. It is the primary goal of this review to examine the patterns of change followed by lipocalins through their complex history, in order to stimulate scientists in the field to experimentally contrast our phylogeny-derived hypotheses. We reexamine our previous work on lipocalin phylogeny and update the phylogenetic analysis of the family. Lipocalins separate into 14 monophyletic clades, some of which are grouped in well supported superclades. The lipocalin tree was rooted with the bacterial lipocalin genes under the assumption that they have evolved from a single common ancestor with the metazoan lipocalins, and not by horizontal transfer. The topology of the rooted tree and the species distribution of lipocalins suggest that the newly arising lipocalins show a higher rate of amino acid sequence divergence, a higher rate of gene duplication, and their internal pocket has evolved towards binding smaller hydrophobic ligands with more efficiency.     

Exon-intron structure and evolution of the Lipocalin gene family

The Lipocalins are an ancient protein family whose expression is currently confirmed in bacteria, protoctists, plants, arthropods, and chordates. The evolution of this protein family has been assessed previously using amino acid sequence phylogenies. In this report we use an independent set of characters derived from the gene structure (exon-intron arrangement) to infer a new lipocalin phylogeny. We also present the novel gene structure of three insect lipocalins. The position and phase of introns are well preserved among lipocalin clades when mapped onto a protein sequence alignment, suggesting the homologous nature of these introns. Because of this homology, we use the intron position and phase of 23 lipocalin genes to reconstruct a phylogeny by maximum parsimony and distance methods. These phylogenies are very similar to the phylogenies derived from protein sequence. This result is confirmed by congruence analysis, and a consensus tree shows the commonalities between the two source trees. Interestingly, the intron arrangement phylogeny shows that metazoan lipocalins have more introns than other eukaryotic lipocalins, and that intron gains have occurred in the C-termini of chordate lipocalins. We also analyze the relationship of intron arrangement and protein tertiary structure, as well as the relationship of lipocalins with members of the proposed structural superfamily of calycins. Our congruence analysis validates the gene structure data as a source of phylogenetic information and helps to further refine our hypothesis on the evolutionary history of lipocalins.     

Comparative ligand-binding analysis of ten human lipocalins

At least ten different lipocalins occur in the human body: retinol-binding protein (RBP), alpha1-acid glycoprotein, alpha1-microglobulin, apolipoprotein D, beta-trace protein, complement component 8gamma, glycodelin, neutrophil gelatinase-associated lipocalin, odorant-binding protein, and tear lipocalin. Although many of these lipocalins seem to play an important physiological role, their precise biological function is not always clear. Especially the interpretation of their diverse ligand-binding activities has been hampered by the fact that the natural lipocalins were prepared from different sources and with varying purity. Here we present a generic expression and purification strategy for the recombinant lipocalins, which is based on secretion into the periplasm of E. coli, where disulphide bonds are readily formed, followed by affinity purification via the Strep-tag II and gel filtration. The ten human lipocalins were successfully prepared and their ligand-binding activities were compared via fluorescence titration with a set of typical ligands: retinol, retinoic acid (RA), 11-(5-(dimethylamino)-1-naphthalene-sulfonylamino)undecanoic acid (DAUDA), and 8-anilino-1-naphtalene-sulfonic acid (ANS). As result, merely two lipocalins, RBP and beta-trace, revealed high affinities both for retinol and for RA, which probably reflects a specialized physiological function in retinoid complexation. Surprisingly, the strongest retinol affinity was detected for apolipoprotein D, whereas this lipocalin exhibits much weaker binding activity for retinoic acid. Binding studies with the two spectroscopic probes DAUDA and ANS revealed mixed patterns, which demonstrates that the affinity for lipophilic substances varies considerably among human lipocalins. Notably, RBP with its perfectly moulded retinol-binding site did not show any detectable binding activity for both compounds. Hence, our recombinant expression and purification system should be useful for further structural and functional studies of lipocalins from human origin and beyond.     

Lipocalins and cancer

Lipocalins are mainly extracellular carriers of lipophilic molecules, though exceptions with properties like prostaglandin synthesis and protease inhibition are observed for specific lipocalins. The interest concerning lipocalins in cancer has so far been focussed to the variations in concentration and the modification of lipocalin expression in distinct cancer forms. In addition, lipocalins have been assigned a role in cell regulation. The influence of the extracellular lipocalins on intracellular cell regulation events is not fully understood, but several of the lipocalin ligands are also well-known agents in cell differentiation and proliferation. Lipophilic ligands can, after lipocalin-mediated transport to the cell surface, penetrate the cell membrane and interact with proteins in the cytosol and/or the nucleus. The signaling routes of the lipocalin ligands, retinoids and fatty acids are presented and discussed. Tumor growth in tissue is restricted by extracellular protease/protease inhibitor interactions. Several lipocalins also have protease inhibitory properties and possess the ability to interact with tumor specific proteases, revealing another pathway for lipocalins to interact with cancer cells.     

The lipocalin protein family: structural and sequence overview

Lipocalins are remarkably diverse at the sequence level yet have highly conserved structures. Most lipocalins share three characteristic conserved sequence motifs - the kernel lipocalins - while others are more divergent family members - the outlier lipocalins - typically sharing only one or two. This classification is a useful tool for analysing the family, and within these large sets are smaller groups sharing much higher levels of sequence similarity. The lipocalins are also part of a larger protein superfamily: the calycins, which includes the fatty acid binding proteins, avidins, a group of metalloproteinase inhibitors, and triabin. The superfamily is characterised by a similar structure (a repeated +1 topology beta-barrel) and by the conservation of a remarkable structural signature.     

Exon-intron structure of outlier tick lipocalins indicate a monophyletic origin within the larger lipocalin family

All tick proteins assigned to the lipocalin family lack the structural conserved regions (SCRs) that are characteristic of the kernel lipocalins and can thus be classified as outliers. These tick proteins have been assigned to the tick lipocalin family based on database searches that indicated homology between tick sequences and the fact that the histamine binding protein (HBP2) from the hard tick Rhipicephalus appendiculatus (Ixodidae) shows structural similarity to the lipocalin fold. Sequence identity between kernel and outlier lipocalins falls below 20% and the question raised is whether the outlier and kernel lipocalins are truly homologous. More specifically in the case of the tick lipocalins, whether their structural fold is derived from the lipocalin fold or whether convergent evolution resulted in the generation of the basic lipocalin-like fold which consists of an eight stranded continuous anti-parallel beta-barrel terminated by a C-terminal alpha-helix that lies parallel to the barrel. The current study determined the gene structure for HBP2 and TSGP1, TSGP2 and TSGP4, lipocalins identified from the soft tick Ornithodoros savignyi (Argasidae). All tick lipocalins have four introns (A-D) with conserved positions and phases within the tick lipocalin sequence alignment. The positions and phase information are also conserved with regard to the rest of the lipocalin family. Phylogenetic analysis using this information shows conclusively that tick lipocalins are evolutionary related to the rest of the lipocalin family. Tick lipocalins are grouped within a monophyletic clade that indicates a monophyletic origin within the tick lineage and also group with the other arthropod lipocalins in a larger clade. Phylogenetic analysis of sequence alignments based on conserved secondary structure of the lipocalin fold support the conclusions from the gene structure trees. These results indicate that exon-intron arrangement can be useful for the inclusion of outlier lipocalins within the larger lipocalin family.     

The bacterial lipocalins

The lipocalins were once regarded as a eukaryotic protein family, but new members have been recently discovered in bacteria. The first bacterial lipocalin (Blc) was identified in Escherichia coli as an outer membrane lipoprotein expressed under conditions of environmental stress. Blc is distinguished from most lipocalins by the absence of intramolecular disulfide bonds, but the presence of a membrane anchor is shared with two of its closest homologues, apolipoprotein D and lazarillo. Several common features of the membrane-anchored lipocalins suggest that each may play an important role in membrane biogenesis and repair. Additionally, Blc proteins are implicated in the dissemination of antibiotic resistance genes and in the activation of immunity. Recent genome sequencing efforts reveal the existence of at least 20 bacterial lipocalins. The lipocalins appear to have originated in Gram-negative bacteria and were probably transferred horizontally to eukaryotes from the endosymbiotic alpha-proteobacterial ancestor of the mitochondrion. The genome sequences also reveal that some bacterial lipocalins exhibit disulfide bonds and alternative modes of subcellular localization, which include targeting to the periplasmic space, the cytoplasmic membrane, and the cytosol. The relationships between bacterial lipocalin structure and function further illuminate the common biochemistry of bacterial and eukaryotic cells.