植物几丁质酶的结构,基因及其表达

几丁质酶按其蛋白氨基酸序列结构的特征及同源性可分为六类,即：ＣｌａｓｓⅠ－Ⅵ。ＣｌａｓｓＩ在蛋白氨基酸结构上包括三个功能区域,Ｎ－端是富含半胱氨酸的几丁质结合工,约４０个氨基酸;Ｃ－端是酶的催化区,也是酶的主要功能区域,约３００个氨基酸;二者通过一个多变的交联区连接在一起。ＣｌａｓｓⅡ仅具有类似于ＣｌａｓｓⅠ的酶催化区域,而没有几丁质结构区和交联区。ＣｌａｓｓⅢ几丁质酶在氨基酸序列上与ＣｌａｓｓⅠ     

植物几丁质酶的结构、基因及其表达

植物几丁质酶按其蛋白氨基酸序列结构特征及同源性可分为六类,即：ＣｌａｓｓＩ－Ⅵ。ＣｌａｓＩ在蛋白氨基酸结构上包括三个功能区域,Ｎ－端是富含半胱氨酸的几丁质结合区,约４０个氨基酸;Ｃ－端是酶的催化区,也是酶的主要功能区域,约３００个氨基酸;二者通过一个多变的交联区连接在一起。ＣｌａｓｓⅡ仅具有类似于ＣｌａｓｓⅠ的酶催化区域,而没有几丁质结合区和交联区。ＣｌａｓｓⅢ几丁质酶在氨基酸序列上与ＣｌａｓｓⅠ和Ⅱ没有任何同源性,其中有些具有几丁质酶和溶菌酶双重活性。ＣｌａｓｓⅣ类似于ＣｌａｓｓⅠ,只是在几丁质结合区和催化区缺失了少数氨基酸。ＣｌａｓｓＶ类似于ＣｌａｓｓⅠ,但具有两个重复的几丁质结合区。ＣｌａｓＶＩ与前五类几丁质酶无同源性,但与微生物几丁质酶有同源性。所有的植物几丁质酶都是由一个小的多基因族编码的,一般基因中有二个内含子,都位于催化区内。几丁质酶的表达受病原物和植物激素的诱导而表达,也与植物的发育有关。通过转几丁质酶基因的工程植株分析几丁质酶基因的启动子,已鉴定出负责几丁质酶表达的调控序列。     

植物病原细菌Pseudomonas syringae pv. tomato基因组中的信号肽分析

应用SignalP 3.0 对植物病原细菌Pseudomonas syringae pv. tomato DC3000菌株基因组中的全部5 615个ORFs进行了分析,确定其中679个ORFs所编码蛋白质的N-端有信号肽序列,其中已经命名并有注释的有107个ORFs。信号肽的长度以19 ~31 个氨基酸居多,其中最多的是23 个氨基酸的信号肽。具有信号肽的ORFs编码蛋白的长度大多为101~400 个氨基酸之间。同时,对组成信号肽的氨基酸种类作了系统的分析,发现组成信号肽的氨基酸中非极性氨基酸占48.54%,极性氨基酸占18.67%,带负电荷氨基酸占24.54%,带正电荷氨基酸仅占8.00%,出现最多的3种氨基酸依次为亮氨酸、丙氨酸和丝氨酸,最少的氨基酸是异亮氨酸,在切割位点-1端的氨基酸中83.211%均为丙氨酸,在切割位点后3位的氨基酸中最多的氨基酸也是丙氨酸。通过分析确定628个分泌类信号肽,36个信号肽具有RR-motif的保守区段,15个脂蛋白类信号肽,未发现Prepilin-like 信号肽和Bacteriocin and Pheromone信号肽。     

东亚飞蝗中肠几丁质酶基因的克隆、序列分析及组织定位

通过RACE方法,克隆了东亚飞蝗Locusta migratoria manilensis (Meyen)几丁质酶基因 (LmChi)cDNA全序列 (GenBank 登录号：EF092841)。获得的cDNA全长1 604 bp,其中可读框1 452 bp, 编码483个氨基酸。推测其氨基酸序列与18家族昆虫几丁质酶有较高的相似性。与其他几丁质酶一样,东亚飞蝗几丁质酶序列也包含一个信号肽、一个几丁质酶活性位点、一个碳端丝氨酸富集区和一个几丁质结合域。半定量RT-PCR研究表明,LmChi基因只在东亚飞蝗不同发育阶段的中肠组织中表达,而在东亚飞蝗体壁、前肠和后肠均没有发现LmChi基因的转录。     

全基因组预测多粘类芽孢杆菌SC2的分泌蛋白

为了解多粘类芽孢杆菌(Paenibacillus polymyxa)分泌蛋白的典型特征,本研究通过SignalP、ProtCompB、TMHMM、Phobius、LipoP、TatP、MEME和BLAST等多种分析程序对多粘类芽孢杆菌SC2菌株的全基因组共5 439条蛋白质序列进行生物信息的综合分析。结果表明,共获得146个具有典型信号肽的SPⅠ(Signal peptidase Ⅰ)分泌蛋白。信号肽序列中出现频率最高的氨基酸依次是亮氨酸、丙氨酸和丝氨酸。对信号肽的切割位点分析发现与枯草芽孢杆菌等一致,均为A-X-A型。通过MEME对信号肽序列进行分析发现存在一种保守基序。最后用BLAST分析发现,在146个分泌蛋白中,89个具有功能描述的分泌蛋白,主要是细胞生长代谢及生物降解酶类,其余57个皆为功能尚未明确的假定蛋白。本研究获得了多粘类芽孢杆菌SC2菌株分泌蛋白的信息,为进一步研究多粘类芽孢杆菌的蛋白功能奠定了基础。     

西伯利亚蓼几丁质酶基因Class Ⅳ的克隆及生物信息学分析

根据西伯利亚蓼抑制消减文库（SSH）中获得的几丁质酶（CHI）基因的部分序列,采用RACE技术克隆了具完整编码区的cDNA序列,基因全长1017bp,开放阅读框编码270个氨基酸。序列分析表明,该基因的编码蛋白（PsCHI1）以前体形式存在,N端分别有22个氨基酸的信号肽和35个氨基酸的几丁质结合域（CBD）,C端199个氨基酸为催化区（CD）,连接CBD与CD的14个氨基酸为可变交联区,成熟蛋白为不含信号肽部分,呈碱性,带正电荷。PsCHI1与所选其它植物classⅣCHI前体序列具有高度的同源性（53％-69％）,而与classⅠ和classⅡCHI的氨基酸序列同源性较低,推测为植物classⅣCHI。根据日本水稻CHI晶体结构构建了PsCHI1三维分子模型,分析显示PsCHI1可以识别比classⅠ和classⅡCHI短的几丁质片段,并以其它植物CHI的已知结构域和功能为基础,确定PsCHI1具有能够水解真菌细胞壁的结构,推测其可能有抗病原微生物的功能。     

一株Sanguibacter sp.C4产几丁质酶基因的克隆与表达

Chi58是Sanguibacter sp．strain C4产生的一种胞外几丁质酶。通过chiA的特异性PCR引物探测到菌株C4中存在几丁质酶,并将扩增到的几丁质酶基因片段（chiA-F）克隆、测序后,提交GenBank数据库进行同源性搜索。对从GenBank中获得的高同源性序列进行比对,并根据保守区域设计2对PCR引物进行嵌套PCR,扩增出Chi58基因的开放阅读框（ORF）。测序结果表明该酶的ORF由1692个核苷酸组成,编码563个氨基酸,在N端有23个氨基酸的信号肽,其成熟蛋白的分子量应为58．544kDa。对其推导氨基酸的序列分析表明Chi58与沙雷氏菌的几丁质酶（如徂）有高度同源性（88．9％-99．6％）,其结构主要包括信号肽序列、PKD结构域和18家族糖苷水解酶结构域。将该基因克隆到pET32a（＋）载体构建重组质粒pChi58,转入大肠杆菌BL-21（DE3）进行融合表达。经IPTG诱导后,可见分子量约81．1kDa的融合蛋白的表达。     

高羊茅FaChit1基因cDNA克隆及诱导表达

应用简并RT-PCR及RACE技术,从高羊茅中克隆了1个Ⅰ类几丁质酶基因cDNA全长序列,命名为FaChit1.结果表明,该cDNA具有1个951 bp的完整编码框,编码316个氨基酸,其编码产物和其它植物的Ⅰ类几丁质酶在氨基酸序列上具有较高的同源性,包含典型的几丁质结合区、催化区以及脯氨酸、半胱氨酸富集的铰链区,但缺少定位到植物液泡所必须的C末端延伸区靶向信号.Northern杂交显示,FaChit1对真菌激发子有较强的响应,乙烯和干旱胁迫均能有效诱导FaChit1基因的表达,而对机械损伤处理的反应比较微弱,只在叶片中积累少量的mRNA.     

一步法RT—PCR克隆水稻线粒体磷转运蛋白基因及其序列特征分析

以水稻广亲和品种Cpslo17幼穗为材料,用一步法RT—PCR（逆转录聚合酶链式反应）克隆了一个长度为1118bp的编码线粒体磷转运蛋白的OsMPT基因。序列分析表明其包含了基因完整的编码序列,编码由368个氨基酸组成的线粒体磷转运蛋白,它与玉米、大豆、Lotus japonicus、Betula pendula、拟南芥的线粒体磷转运蛋白氨基酸序列相似率分别为93．5％,85．6％,83．8％,83．7％,81．1％。氨基酸疏水谱分析显示它有线粒体磷转运蛋白家族高度保守的6个跨膜结构域。水稻线粒体磷转运蛋白N端富含精氨酸（Arginine）、丙氨酸（Alanine）和丝氨酸（Serine）。iPSORT预测其蛋白N端具有定位于线粒体的信号肽序列,进一步分析表明此编码区段有6个外显子和5个内含子。RT—PCR结果表明,OsMPT基因在水稻两个亚种粳稻和籼稻的叶片中均有表达,在Cpslo17营养器官和生殖器官中都有高水平表达。水稻线粒体磷转运蛋白的克隆和表达分析将为研究其结构和生物学功能奠定基础。     

一株拮抗香蕉枯萎病的内生细菌的分离及其几丁质酶基因信号肽的分泌活性分析

目的：旨在分离并选择一株香蕉内生细菌作为内生基因工程生防菌,并克隆其几丁质酶基因的信号肽序列。方法：从香蕉植株杆下部分离并选择了一株拮抗香蕉枯萎病且具有分泌几丁质酶能力的内生细菌,对该菌株进行了形态观察、生理生化测定和16S rDNA序列分析,克隆了其几丁质酶基因的编码序列并预测了其信号肽,构建了含有信号肽和不含信号肽的几丁质酶的表达菌株BL-chi1和BL-chi2。结果：结合形态观察、生理生化特征和16S rDNA序列比对分析确定该菌株为Klebsiella属,将该菌株命名为KKWB 5;BL-chi1和BL-chi2经IPTG诱导后,均表达了与预期蛋白大小一致的蛋白,同时BL-chi1诱导后的培养基上清中出现一条约45kDa的条带,而BL-chi2和空载体的BL-pET22b诱导后的培养基上清中均无此条带;几丁质水解试验发现,BL-chi1诱导后的培养基上清中的蛋白经浓缩和纯化后都能在几丁质平板上形成透明水解圈。结论：该几丁质酶的信号肽能被BL21（DE3）所识别,将几丁质酶分泌到培养基中,并且分泌的几丁质酶具有水解几丁质的生物学活性。内生菌KKWB-5的分离及其几丁质酶分泌信号肽序列的克隆为进一步构建内生工程菌来防治香蕉枯萎病打下了基础。     

The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis

The GH3 gene family in Arabidopsis, implicated in hormonal homeostasis through the conjugation of indolacetic and jasmonic acids to amino acids, is involved in a broad range of plant growth and development processes. In this work, the analysis of the GH3 family in the genome of Oryza sativa identified 13 hypothetical ORFs. EST analysis and RT-PCR assays demonstrated that 12 of them were active genes. An extensive EST analysis of the GH3 family performed on 26 plant species was used to estimate the minimum number of GH3 genes en each one. The data indicated that the members of the GH3 family progressively increased in the different plant divisions from Chlorophyta (0), Bryophyta (3), and Coniferophyta (4), to Magnoliophyta (7-19). Phylogenetic analyses showed a high degree of conservation between Arabidopsis and rice GH3 proteins and, in general, in the plant kingdom. The data revealed a homology clustering consistent with the functional classification of the Arabidopsis proteins, since most of the 110 sequences analyzed grouped into 2 main clusters, corresponding to the Arabidopsis functional groups I (jasmonic acid adenylation) and II (indolacetic acid adenylation). And additional cluster including group III (non-adenylation ability) was exclusively composed of proteins from Arabidopsis thaliana, Brassica napus and Gossypium hirsutum.     

Non-universal usage of the leucine CUG codon and the molecular phylogeny of the genus Candida

CUG, a universal leucine codon, was reported to be read as serine in 10 species of the genus Candida. We used an in vitro cell-free translation system to identify the amino acid assignment of codon CUG in 78 species and 7 varieties of galactose-lacking Candida species equipped with Q9 as the major ubiquinone. Of these, only 11 species used codon CUG as a leucine codon. The remaining species decoded CUG as serine. Their small subunit ribosomal DNA sequences were also determined and analyzed using both Neighbor-Joining and Maximum Likelihood methods. The species decoding CUG as serine and leucine formed distinct clusters on both molecular phylogenetic trees. Our result suggests that non-universal decoding is not a rare event, and that it is widely distributed in the genus Candida.     

Metabolic diversity in the grains of Indian varieties of rice

The aim of the present work was to analyze metabolic diversity in 26 different indica varieties of rice grains. Seventy-six metabolites could be identified in the methanol extracts of each of the rice varieties analyzed by gas chromatography-mass spectrometry. These metabolites included 9 sugars/sugar alcohols, 17 amino acids/derivatives, 18 fatty acids, 5 free phenolic acids and 19 other organic acids, 3 phytosterols, 5 other constituents. Cluster analyses to extract information for similarity and differences in metabolites unveiled diversity in metabolite profile. Two hierarchical clusters were generated based on the metabolite contents of the rice varieties. The first cluster (cluster I) consisted of one variety only. The second cluster again segregated into four clusters (clusters II, III, IV and V). Very distinct differences were visible amongst the clusters with respect to their sugars/sugar alcohols, organic acid, amino acid and fatty acid, phenol, and sterol profiles. Metabolites determine nutritional quality, taste, aroma. This and future efforts on the metabolomic information would help biochemists and nutritionists to better understand the nutritional quality of such grains at varietal level and correlating metabolites and long term human health related issues.     

Identification of two novel clusters of ultrahigh-sulfur keratin-associated protein genes on human chromosome 11

We analyzed two novel clusters of keratin-associated protein (KAP) genes on human chromosome 11 (11p15.5 and 11q13.5) in which we identified two known human KRTAP5 genes, KerA (=KRN1) and KerB, and nine novel KRTAP5 family genes. RT-PCR analysis of these KAP genes showed preferential expression in human hair root, suggesting these gene products are required for hair formation. Based on the deduced amino acid sequences, all these KAP proteins were classified into an ultrahigh-sulfur (UHS) type KAP with high cysteine content (> 30 mol%). These KAPs also showed high glycine and serine contents (average 24.30 and 21.13 mol%, respectively), distinguishing from other UHS/HS KAP families located on human chromosomes 17 and 21. Dot-matrix analysis revealed a significant similarity between these two KAP gene clusters. We postulated a mechanism by which these two KAP gene clusters are generated via genomic duplication of a primordial gene cluster followed by genetic modification during evolution.     

Thermophilic anaerobic amino acid degradation: deamination rates and end-product formation

Anaerobic thermophilic degradation of several amino acids was studied in batch cultures using an inoculum from a steady-state semicontinuous enrichment culture. Experiments were done in the presence and absence of methanogenesis and known electron acceptors in the Stickland reaction. Methanogenesis was found to be crucial for the degradation of amino acids known to be oxidatively deaminated (leucine, valine and alanine). Other amino acids (serine, threonine, cysteine and methionine) were degraded under both methanogenic and non-methanogenic conditions. Degradation rates for these four amino acids were 1.3 to 2.2 times higher in cases where methanogenesis was active. The degradation rates of serine, threonine, cysteine and methionine were about twice as high as the rates of leucine, valine and alanine under methanogenic conditions. Inclusion of different electron acceptors, known to work in the Stickland reaction, did not enhance the degradation rates of any amino acid used nor did they alter the degradation patterns. Glycine was oxidatively deaminated to acetate, carbon dioxide, hydrogen and ammonium.     

Processing of the Hepatitis C virus precursor protein expressed in the methylotrophic yeast Pichia pastoris

In this paper, the base frequency at the second codon position of the 3839 open reading frames (ORFs) in the Vibrio cholerae genome is analyzed. It is shown that according to the base content at this codon site, the ORFs can be divided into two clusters, each containing 673 and 3166 ORFs, respectively. ORFs in the smaller cluster usually have significantly higher T frequency than that of A at the second codon position. For the two clusters of ORFs, there are significant differences in the frequencies for 18 of the 20 amino acids in the encoding proteins. The two clusters of ORFs are also significantly different in their functions. More than half of the known genes involved in transport and binding are included in the smaller cluster, while few genes involved in amino acid biosynthesis, protein synthesis, and so on are included in this cluster.     

Lipoic acid-dependent oxidative catabolism of alpha-keto acids in mitochondria provides evidence for branched-chain amino acid catabolism in Arabidopsis

Lipoic acid-dependent pathways of alpha-keto acid oxidation by mitochondria were investigated in pea (Pisum sativum), rice (Oryza sativa), and Arabidopsis. Proteins containing covalently bound lipoic acid were identified on isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis separations of mitochondrial proteins by the use of antibodies raised to this cofactor. All these proteins were identified by tandem mass spectrometry. Lipoic acid-containing acyltransferases from pyruvate dehydrogenase complex and alpha-ketoglutarate dehydrogenase complex were identified from all three species. In addition, acyltransferases from the branched-chain dehydrogenase complex were identified in both Arabidopsis and rice mitochondria. The substrate-dependent reduction of NAD(+) was analyzed by spectrophotometry using specific alpha-keto acids. Pyruvate- and alpha-ketoglutarate-dependent reactions were measured in all three species. Activity of the branched-chain dehydrogenase complex was only measurable in Arabidopsis mitochondria using substrates that represented the alpha-keto acids derived by deamination of branched-chain amino acids (Val [valine], leucine, and isoleucine). The rate of branched-chain amino acid- and alpha-keto acid-dependent oxygen consumption by intact Arabidopsis mitochondria was highest with Val and the Val-derived alpha-keto acid, alpha-ketoisovaleric acid. Sequencing of peptides derived from trypsination of Arabidopsis mitochondrial proteins revealed the presence of many of the enzymes required for the oxidation of all three branched-chain amino acids. The potential role of branched-chain amino acid catabolism as an oxidative phosphorylation energy source or as a detoxification pathway during plant stress is discussed.     

Comparative phylogenetic analysis of cystatin gene families from arabidopsis,rice and barley

The plant cystatins or phytocystatins comprise a family of specific inhibitors of cysteine proteinases. Such inhibitors are thought to be involved in the regulation of several endogenous processes and in defence against pests and pathogens. Extensive searches in the complete rice and Arabidopsis genomes and in barley EST collections have allowed us to predict the presence of twelve different cystatin genes in rice, seven in Arabidopsis, and at least seven in barley. Structural comparisons based on alignments of all the protein sequences using the CLUSTALW program and searches for conserved motifs using the MEME program have revealed broad conservation of the main motifs characteristic of the plant cystatins. Phylogenetic analyses based on their deduced amino acid sequences have allowed us to identify groups of orthologous cystatins, and to establish homologies and define examples of gene duplications mainly among the rice and barley cystatin genes. Moreover, the absence of a counterpart between the two monocots, as well as strong variations in the motifs that interact with the cysteine proteinases, may be related to a species-specific evolutionary process. This cystatin classification should facilitate the assignment of proteinase specificities and functions to other cystatins as new information is obtained.Electronic Supplementary Material Supplementary material is available for this article at     

The screening and preliminary construction of quality mutant population for cultivar “Nipponbare” in japonica rice (Oryza sativa)

Progenies of Oryza sativa cv. Nipponbare induced with 0.4% ethyl methane sulphonate (EMS) were screened for quality mutants and the preliminary quality mutant population was constructed in present experiment. A total of 2210 materials were first screened using near infrared reflectance spectroscopy (NIRS) from which 208 quality mutants were obtained for a second screening and then yielded 73 quality mutants including amylase content (AC), gel consistency (GC), gelatinization temperature (GT), protein content (PC), rapid viscosity analysis (RVA) parameters and amino acid contents. The screening yielded 11 PC mutants with a mutation frequency of 4.98??, followed by 7 rice floury viscosity mutants (3.17??), 5 AC mutants (2.26??), 4 chalky mutants, GT and GC mutants (1.81??), and 2 ASV mutants (0.9??). The relative contents of 17 kinds of amino acid mutations, including 7 kinds for essential amino acids and 10 kinds for nonessential amino acids were identified. With the variation of 10% as the screening standard, mutants were obtained for lysine and leucine at 0.45?? and for valine at 4.98??, but no mutants were found for isoleucine, phenylalanine, threonine. For nonessential amino acids, mutants of glutamic (0.45??), arginine (3.62??), alanine (3.17??), serine (0.45??), glycine (0.45??), tyrosine (1.81??), proline (2.71??), and histidine (0.45??) were obtained, but none was found for aspartic, phenylalanine nor threonine. At 100% as the screening standard for methionine and cysteines, the mutation frequency of these two amino acid mutants were 0.9?? and 4.98?? respectively. Quality mutants in this preliminary library of rice could play important role in gene function and breeding of rice quality.