Signal peptide prediction based on analysis of experimentally verified cleavage sites

A number of computational tools are available for detecting signal peptides, but their abilities to locate the signal peptide cleavage sites vary significantly and are often less than satisfactory. We characterized a set of 270 secreted recombinant human proteins by automated Edman analysis and used the verified cleavage sites to evaluate the success rate of a number of computational prediction programs. An examination of the frequency of amino acid in the N-terminal region of the data set showed a preference of proline and glutamine but a bias against tyrosine. The data set was compared to the SWISS-PROT database and revealed a high percentage of discrepancies with cleavage site annotations that were computationally generated. The best program for predicting signal sequences was found to be SignalP 2.0-NN with an accuracy of 78.1% for cleavage site recognition. The new data set can be utilized for refining prediction algorithms, and we have built an improved version of profile hidden Markov model for signal peptides based on the new data.     

Characterization of the cleavage of signal peptide at the C-terminus of hepatitis C virus core protein by signal peptide peptidase

Production of hepatitis C virus (HCV) core protein requires the cleavages of polyprotein by signal peptidase and signal peptide peptidase (SPP). Cleavage of signal peptide at the C-terminus of HCV core protein by SPP was characterized in this study. The spko mutant (mutate a.a. 189–193 from ASAYQ to PPFPF) is more efficient than the A/F mutant (mutate a.a 189 and 191 from A to F) in blocking the cleavage of signal peptide by signal peptidase. The cleavage efficiency of SPP is inversely proportional to the length of C-terminal extension of the signal peptide: the longer the extension, the less efficiency the cleavage is. Thus, reducing the length of C-terminal extension of signal peptide by signal peptidase cleavage could facilitate further cleavage by SPP. The recombinant core protein fused with signal peptide from the C-terminus of p7 protein, but not those from the C-termini of E1 and E2, could be cleaved by SPP. Therefore, the sequence of the signal peptide is important but not the sole determinant for its cleavage by SPP. Replacement of the HCV core protein E.R.-associated domain (a.a. 120–150) with the E.R.-associated domain (a.a.1–50) of SARS-CoV membrane protein results in the failure of cleavage of this recombinant protein by SPP, though this protein still is E.R.-associated. This result suggests that not only E.R.-association but also specific protein sequence is important for the HCV core protein signal peptide cleavage by SPP. Thus, our results suggest that both sequences of the signal peptide and the E.R.-associated domain are important for the signal peptide cleavage of HCV core protein by SPP. Electronic Supplementary MaterialThe online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

基于转录组解析淡玫红鹅膏环肽基因家族特征及其系统发育

【背景】淡玫红鹅膏(Amanita pallidorosea)是鹅膏属檐托鹅膏组的一种剧毒鹅膏菌,其子实体内含有丰富的鹅膏环肽毒素,但其编码毒环肽和相关肽的基因家族"MSDIN"尚待深入研究。【目的】探究淡玫红鹅膏中编码毒环肽及相关肽的基因家族成员的多样性、保守性及其系统发育。【方法】采用Illumina HiSeq2000平台对淡玫红鹅膏转录组进行测序,使用TBLASTn软件对MSDIN基因家族进行检索,并设计特异性引物进行PCR验证,通过生物信息学比对分析MSDIN基因家族成员的种类和序列构成,通过重建分子系统发育树了解其演化历程。【结果】通过对MSDIN基因家族的查找,从转录组数据获得了60条环肽编码基因,经PCR验证其可编码32条环肽,包括α-鹅膏毒肽、β-鹅膏毒肽和羧基二羟鬼笔毒肽。本研究报道了8条新环肽。分子系统发育树分析显示,鹅膏环肽分为鹅膏毒肽、鬼笔毒肽和未知功能环肽3大支。系统发育结合保守序列推测出7条潜在的新毒肽。【结论】淡玫红鹅膏具有丰富的鹅膏环肽资源,利用转录组测序能够系统挖掘鹅膏环肽新资源,为其整体结构解析奠定基础。     

内生菌KM-1-2全基因组ORFs信号肽和分泌蛋白预测及功能分析

【目的】内生菌普遍存在于植物中,与宿主在长期的进化中形成了互利共生的关系。目前对内生菌和植物之间的互作机制研究较少,为深入了解银杏叶内生菌KM-1-2与寄主植物作用机制,本研究对其分泌蛋白进行预测,并明确其特征。【方法】组合使用信号肽分析软件Signal P,跨膜螺旋结构分析软件TMHMM 2.0和Phobius,蛋白质细胞定位软件PSORT,亚细胞定位软件Target P和GPI锚定位点分析软件big-PI Predictor,预测KM-1-2基因组范围内所有分泌蛋白,定义为分泌组。【结果】KM-1-2全基因组5299条蛋白序列中发现271个具有典型信号肽的分泌蛋白,占全基因组的2.4%;编码这些蛋白的ORF最短为61 bp,最大为2105 bp,平均为373 bp;引导它们的信号肽长度分布在15–37 aa之间,平均为24 aa。信号肽中出现频率最高的氨基酸依次为丙氨酸、亮氨酸和缬氨酸,信号肽切割类型多属于A-X-A型,即SPI切割类型。共66个蛋白质有功能描述,其中包括26个酶类。这些酶主要包括各种糖苷水解酶、酯酶、蛋白酶、碳氧裂解酶等。【结论】通过上述生物信息学分析方法有效实现了银杏叶内生菌KM-1-2分泌蛋白的预测,这些分泌蛋白功能涉及较多的酶类以及其他未知功能,为进一步研究内生菌和植物的互作提供了基础。     

Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage

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精-甘-天冬-丝氨酸四肽对二磷酸腺苷诱导大鼠血小板活化的信号转导的影响

本工作在二磷酸腺苷（ＡＤＰ）活化的大鼠血小板上,观察精－甘－天冬－丝上肽（ＲＧＤＳ肽）对血小板聚集、蛋白磷酸化、蛋白激酶Ｃ和丝裂素活化蛋白激酶活性的影响。结果发现,５０μｍｏｌ／ＬＡＤＰ引起血小板聚集时,蛋白激酶Ｃ（ＰＫＣ０及丝裂经蛋白激酶（ＭＡＰＫ）活性增加,并引起９５和６６ｋＤ蛋白磷酸化。应用５０,１００和２００μｍｏｌ／ＬＲＧＤＳ肽与基共同孵育,呈浓度依赖地抑制ＡＤＰ引起的血小板聚集和对ＰＫ     

Molecular phylogeny of Flaveria as deduced from the analysis of nucleotide sequences encoding the H-protein of the glycine cleavage system

Sequence comparisons have shown that nucleotide sequences of the H-protein, a component of the glycine cleavage system, are only moderately conserved and can be used as molecular markers for intrageneric phylogenetic studies. We have analysed the respective cDNA sequences from 12 species of Flaveria, and a more limited set of gdcsH upstream regions. These data are discussed with respect to a phylogenetic reconstruction of Flaveria, a small genus which includes species of different photo-synthetic types, namely C₃, C₃-C₄, C₄-like and C₄. Our analysis essentially supports an earlier hypothesis, based on morphological and eco-geographical data, of the evolution of Flaveria (Powell 1978). This close agreement shows the usefulness of H-protein nucleotide sequences at a low taxonomic level. Our analysis independently confirms that C₄ photosynthesis has evolved two times in different lineages of Flaveria. Most remarkably, the C₄ taxa of Flaveria appear as derived relative to the C₃-C₄ intermediate taxa, i.e. they probably have common direct predecessors. This is the first direct evidence for a phylo-genetically intermediate position of C₃-C₄ intermediate photosynthesis. Our data also confirm the antiquity of C₃ photosynthesis in Flaveria but suggest that the collection of F.pringlei used in our experiments, although clearly of C₃ photosynthetic metabolism, possibly originated from hybridization with a more advanced taxon.     

ATP modulation of the ligand binding and signal transduction activities of the type C natriuretic peptide receptor guanylate cyclase

The type C natriuretic peptide (CNP)-activated guanylate cyclase (CNP-RGC) is a single-chain transmembrane-spanning protein, containing both CNP binding and catalytic cyclase activities. Upon binding CNP to the extracellular receptor domain, the cytosolic catalytic domain of CNP-RGC is activated, generating the second messenger cyclic GMP. Obligatory in this activation process is an intervening signal transduction step which is regulated by ATP binding to the cyclase. This bridges the events of ligand binding and cyclase activation. A defined sequence motif (Gly⁴⁹⁹-Xa-Xa-Xa-Gly⁵⁰³), termed ATP regulatory module (ARM), is critical for this step. The present study shows that ATP not only amplifies the signal transduction step, it also concomitantly reduces the ligand binding activity of CNP-RGC. Reduction in the ligand binding activity is a consequence of the transformation of the high affinity receptor-form to the low affinity receptor-form. A single ARM residue Gly⁴⁹⁹ is critical in the mediation of both ATP effects, signal transduction and ligand binding activity of the receptor. Thus, this residue represents an ATP bimodal switch to turn the CNP signal on and off.     

Phylogenetic analysis of chinese rhesus macaques (Macaca mulatta) based on mitochondrial control region sequences

Between one and six subspecies of Chinese rhesus macaques (Macaca mulatta) have been proposed based on morphological differences and/or their geographic distribution. In this study, a 489 base pair fragment of the mitochondrial control region was amplified from 230 DNA samples collected from rhesus macaques in the Sichuan province in Western China. The fragment was then sequenced and aligned with 208 sequences from wild rhesus macaques, sampled throughout the species' geographic range in China downloaded from GenBank. Phylogenetic analysis of the 182 unique sequences identified among these samples divided Chinese rhesus macaques into two western haplogroups (haplogroups A and B) and three older eastern haplogroups (haplogroups C, D, and E), whose differentiation probably occurred during the penultimate glacial event. During the warming after the penultimate glacial event, haplogroups A, B, and E rapidly expanded and a relatively young subhaplogroup of haplogroup E, E', limited to Southern China but shared with Vietnamese rhesus macaques, was reintroduced from Indochina during the last glacial event. One haplotype most closely related to subhaplogroup E' probably represents the isolation of Hainan Island, to where it is restricted, from the mainland by the formation of the Qiongzhou Strait approximately 8,500 years ago. The distribution of haplogroups both informs the phylogeographic history of dispersal of Chinese rhesus macaques and has implications for their suitability as animal models in biomedical research.     

Mutagenesis of the glucoamylase signal peptide of Saccharomyces diastaticus and functional analysis in Saccharomyces cerevisiae

To improve the efficiency of the glucoamylase signal peptide (GSP) of Saccharomyces diastaticus for the secretion of foreign proteins, hybrid plasmids containing one of four types of GSP mutant (m1, Pro(-18)-->Leu(-18); m2, Tyr(-13)-->Leu(-13); m3, Ser(-9)-->Leu(-9); m4, Asn(-5)-->Pro(-5)) were constructed and evaluated in Saccharomyces cerevisiae using Bacillus endo-1,4-beta-D-glucanase (CMCase) as a reporter gene. CMCase secretion by m1, m2 and m3 GSP mutants was increased, likely resulting from a higher probability of the modified GSP to assume an alpha-helical structure. Especially in the case of m3, the substitution of Leu for a polar residue, Ser(-9), in the hydrophobic region resulted in approximately a twofold increase in extracellular CMCase activity. In mutant 4, which disrupts the alpha-helix of GSP, CMCase was less efficiently secreted.     

Development of an isotope dilution mass spectrometry assay for HbA1c based on enzyme-cleaved peptide analysis

The hydrophobic contributions of 17 individual peptides, fused to the N-terminal of Bacillus stearothermophilus lactate dehydrogenase (LDH) were studied by hydrophobic interaction chromatography (HIC) and aqueous two-phase system (ATPS). The constructs were sequenced from a protein library designed with a five-amino acid randomised region in the N-terminal of an LDH protein. The 17 LDH variants and an LDH control lacking the randomised region were expressed in Escherichia coli. HIC and ATPS behaviour of the proteins indicated significant differences in protein hydrophobicity, even though the modifications caused only 1% increase in protein molecular weight and 2% variation in isoelectric points. HIC and ATPS results correlated well (R(2) = 0.89). Protein expression was clearly affected by N-terminal modification, but there was no evidence that the modification affected protein activity. A GluAsnAlaAspVal modification resulted in increased protein expression. In most cases, HIC and ATPS results compared favourably with those predicted on the basis of 34 amino acid residue hydrophobicity scales; assuming exposure of tag residues to solution. Exceptions included LeuAlaGlyValIle and LeuTyrGlyCysIle modifications, which were predicted, assuming full solution exposure, to be more hydrophobic than observed.     

The influence of phylogeny and life history on telomere lengths and telomere rate of change among bird species: A meta‐analysis

Longevity is highly variable among animal species and has coevolved with other life‐history traits, such as body size and rates of reproduction. Telomeres, through their erosion over time, are one of the cell mechanisms that produce senescence at the cell level and might even have an influence on the rate of aging in whole organisms. However, uneroded telomeres are also risk factors of cell immortalization. The associations of telomere lengths, their rate of change, and life‐history traits independent of body size are largely underexplored for birds. To test associations of life‐history traits and telomere dynamics, we conducted a phylogenetic meta‐analysis using studies of 53 species of birds. We restricted analyses to studies that applied the telomere restriction fragment length (TRF) method, and examined relationships between mean telomere length at the chick (Chick TL) and adult (Adult TL) stages, the mean rate of change in telomere length during life (TROC), and life‐history traits. We examined 3 principal components of 12 life‐history variables that represented: body size (PC1), the slow–fast continuum of pace of life (PC2), and postfledging parental care (PC3). Phylogeny had at best a small‐to‐medium influence on Adult and Chick TL (r ² = .190 and .138, respectively), but a substantial influence on TROC (r ² = .688). Phylogeny strongly influenced life histories: PC1 (r ² = .828), PC2 (.838), and PC3 (.613). Adult TL and Chick TL were poorly associated with the life‐history variables. TROC, however, was negatively and moderate‐to‐strongly associated with PC2 (unadjusted r = −.340; with phylogenetic correction, r = −.490). Independent of body size, long‐lived species with smaller clutches, and slower embryonic rate of growth may exhibit less change in telomere length over their lifetimes. We suggest that telomere lengths may have diverged, even among closely avian‐related species, yet telomere dynamics are strongly linked to the pace of life.     

The phylogenetic position of the Aeolosomatidae and Parergodrilidae, two enigmatic oligochaete-like taxa of the 'Polychaeta', based on molecular data from 18S rDNA sequences

The Aeolosomatidae and the Parergodrilidae are meiofaunal Annelida showing different combinations of clitellate‐like and non‐clitellate character states. Their phylogenetic positions and their systematic status within the Annelida are still in debate. Here we attempt to infer their systematic position using 18S rDNA sequences of the aeolosomatid Aeolosoma sp. and the parergodrilid Stygocapitella subterranea and several other meiofaunal taxa such as the Dinophilidae, Polygordiidae and Saccocirridae. The data matrix was complemented by sequences from several annelid, arthropod and molluscan species. After evaluation of the phylogenetic signal the data set was analysed with maximum‐parsimony, distance and maximum‐likelihood algorithms. Sequences from selected arthropods or molluscs were chosen for outgroup comparison. The resolution of the resulting phylogenies is discussed in comparison to previous studies. The results do not unequivocally support a sister‐group relationship of Aeolosoma sp. and the Clitellata. Instead, depending on the algorithms applied, Aeolosoma clusters in various clades within the polychaetes, for instance, together with eunicidan species, the Dinophilidae, Harmothoë impar or Nereis limbata. The position of Aeolosoma sp. thus cannot be resolved on the basis of the data available. S. subterranea always falls close to a cluster comprising Scoloplos armiger, Questa paucibranchiata and Magelona mirabilis, all of which were resolved as not closely related to both Aeolosoma sp. and the Clitellata. Therefore, convergent evolution of clitellate‐like characters in S. subterranea and hence in the Parergodrilidae is suggested by our phylogenetic analysis. Moreover, the Clitellata form a monophyletic clade within the paraphyletic polychaetes.     

Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences

The two families of the order Apiales (Apiaceae and Araliaceae) represent a classic example of the difficulty in understanding evolutionary relationships between tropical-temperate family pairs. In Apiales, this problem is further compounded by phylogenetic confusion at almost every taxonomic level, including ordinal, interfamilial, and infrafamilial, due largely to difficulties in understanding trends in morphological evolution. Phylogenetic analyses of rbcL sequences were employed to resolve relationships at the ordinal and familial levels. The results of the ordinal analysis confirm the placement of Apiales in an expanded subclass Asteridae as the sister group to Pittosporaceae, and refute the traditional alliance of Apiales with Cornales and Rosidae. This study has also resolved relationships of a number of enigmatic genera, suggesting, for example, that Melanophylla, Aralidium, Griselinia, and Toricellia are close relatives of Apiales. Clarification of phylogenetic relationships has concomitantly provided insights into trends of morphological evolution, and suggests that the ancestral apialean taxon was probably bicarpellate, simple-leaved, woody, and paleotropical. Phylogenetic analysis at the family level suggests that apiaceous subfamily Hydrocotyloideae, often envisioned as an intermediate group between Apiaceae and Araliaceae, is polyphyletic, with some hydrocotyloids closely allied with Araliaceae rather than Apiaceae. With the exception of some hydrocotyloids, Apiaceae appear to be monophyletic. The relationship between Apiaceae and Araliaceae remains problematic. Although the shortest rbcL trees suggest that Apiaceae are derived from within a paraphyletic Araliaceae, this result is only weakly supported.     

利用叶绿体DNA trnL-F序列初步探讨菊科风毛菊属的系统发育

风毛菊属Saussurea DC.是菊科物种分化十分剧烈和分类处理十分困难的一个属。该属的单系起源性质、属下分类系统以及一些独特形态物种的系统位置尚不清楚,有待进一步验证。本文测定了代表该属5个亚属37种植物43个样品和川木香属Dolomiaea DC.的１种样品的叶绿体DNA trnL-F序列,并调取菜蓟族Cardueae Cass.与风毛菊属具有一定亲缘关系的13属的该序列,一起进行了分支分析,重点验证该属的属下形态分类系统以及形态特殊、青藏高原地区特有的雪兔子亚属subgen. Eriocoryne     

Molecular phylogeny of the Heterotrichea (Ciliophora, Postciliodesmatophora) based on small subunit rRNA gene sequences

A comprehensive molecular analysis of the phylogenetic relationships within the Heterotrichea including all described families is still lacking. For this reason, the complete nuclear small subunit (SSU) rDNA was sequenced from further representatives of the Blepharismidae and the Stentoridae. In addition, the SSU rDNA of a new, undescribed species of the genus Condylostomides (Condylostomatidae) was sequenced. The detailed phylogenetic analyses revealed a consistent branching pattern: while the terminal branches are generally well resolved, the basal relationships remain unsolved. Moreover, the data allow some conclusions about the macronuclear evolution within the genera Blepharisma, Stentor, and Spirostomum suggesting that a single, compact macronucleus represents the ancestral state.     

Improving the analysis of dinoflagellate phylogeny based on rDNA

Phylogenetic studies of dinoflagellates are often conducted using rDNA sequences. In analyses to date, the monophyly of some of the major lineages of dinoflagellates remain to be demonstrated. There are several reasons for this uncertainty, one of which may be the use of models of evolution that may not closely fit the data. We constructed and examined alignments of SSU and partial LSU rRNA along with a concatenated alignment of the two molecules. The alignments showed several characteristics that may confound phylogeny reconstruction: paired helix (stem) regions that contain non-independently evolving sites, high levels of compositional heterogeneity among some of the sequences, high levels of incompatibility (homoplasy), and rate heterogeneity among sites. Taking into account these confounding factors, we analysed the data and found that the Gonyaulacales, a well-supported clade, may be the most recently diverged order. Other supported orders were, in the analysis based on SSU, the Suessiales and the Dinophysiales; however, the Gymnodiniales and Prorocentrales appeared to be polyphyletic. The Peridiniales without Heterocapsa species appeared as a monophyletic group in the analysis based on LSU; however, the support was low. The concatenated alignment did not provide a better phylogenetic resolution than the single gene alignments.     

The phylogeny of the Anderson's White‐bellied Rat (Niviventer andersoni) based on complete mitochondrial genomes

The phylogenetic structure of the genus Niviventer has been studied based on several individual mitochondrial and nuclear genes, but the results seem to be inconsistent. In order to clarify the phylogeny of Niviventer, we sequenced the complete mitochondrial genome of white‐bellied rat (Niviventer andersoni of the family Muridae) by next‐generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein‐coding genes (PCGs), two ribosomal RNA genes, and one noncoding control region (D‐Loop). Phylogenetic analyses of the nucleotide sequences of all 13 PCGs, PCGs minus ND6, and the entire mitogenome sequence except for the D‐loop revealed well‐resolved topologies supporting that N. andersoni was clustered with N. excelsior forming a sister division with N. confucianus, which statistically rejected the hypothesis based on the tree of cytochrome b (cytb) gene that N. confucianus is sister to N. fulvescens. Our research provides the first annotated complete mitochondrial genome of N. andersoni, extending the understanding about taxonomy and mitogenomic evolution of the genus Niviventer.