Phylogenetic analysis of uroporphyrinogen III synthase (UROS) gene

The uroporphyrinogen III synthase (UROS) enzyme (also known as hydroxymethylbilane hydrolyase) catalyzes the cyclization of hydroxymethylbilane to uroporphyrinogen III during heme biosynthesis. A deficiency of this enzyme is associated with the very rare Gunther''s disease or congenital erythropoietic porphyria, an autosomal recessive inborn error of metabolism. The current study investigated the possible role of UROS (Homo sapiens [EC: 4.2.1.75; 265 aa; 1371 bp mRNA; Entrez Pubmed ref {"type":"entrez-protein","attrs":{"text":"NP_000366.1","term_id":"4557873","term_text":"NP_000366.1"}}NP_000366.1, {"type":"entrez-nucleotide","attrs":{"text":"NM_000375.2","term_id":"171543867","term_text":"NM_000375.2"}}NM_000375.2]) in evolution by studying the phylogenetic relationship and divergence of this gene using computational methods. The UROS protein sequences from various taxa were retrieved from GenBank database and were compared using Clustal-W (multiple sequence alignment) with defaults and a first-pass phylogenetic tree was built using neighbor-joining method as in DELTA BLAST 2.2.27+ version. A total of 163 BLAST hits were found for the uroporphyrinogen III synthase query sequence and these hits showed putative conserved domain, HemD superfamily (as on 14^th Nov 2012). We then narrowed down the search by manually deleting the proteins which were not UROS sequences and sequences belonging to phyla other than Chordata were deleted. A repeat phylogenetic analysis of 39 taxa was performed using PhyML and TreeDyn software to confirm that UROS is a highly conserved protein with approximately 85% conserved sequences in almost all chordate taxons emphasizing its importance in heme synthesis.     

Phylogenetic analysis of cubilin (CUBN) gene

Cubilin, (CUBN; also known as intrinsic factor-cobalamin receptor [Homo sapiens Entrez Pubmed ref {"type":"entrez-nucleotide","attrs":{"text":"NM_001081.3","term_id":"126091151","term_text":"NM_001081.3"}}NM_001081.3; {"type":"entrez-nucleotide","attrs":{"text":"NG_008967.1","term_id":"212549718","term_text":"NG_008967.1"}}NG_008967.1; GI: 119606627]), located in the epithelium of intestine and kidney acts as a receptor for intrinsic factor – vitamin B12 complexes. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. The current study investigated the possible role of CUBN in evolution using phylogenetic testing. A total of 588 BLAST hits were found for the cubilin query sequence and these hits showed putative conserved domain, CUB superfamily (as on 27^th Nov 2012). A first-pass phylogenetic tree was constructed to identify the taxa which most often contained the CUBN sequences. Following this, we narrowed down the search by manually deleting sequences which were not CUBN. A repeat phylogenetic analysis of 25 taxa was performed using PhyML, RAxML and TreeDyn softwares to confirm that CUBN is a conserved protein emphasizing its importance as an extracellular domain and being present in proteins mostly known to be involved in development in many chordate taxa but not found in prokaryotes, plants and yeast.. No horizontal gene transfers have been found between different taxa.     

Oxysterol binding proteins (OSBPs) and their encoding genes in Arabidopsis and rice

Cell wall deposition, biosynthesis of steroid hormones, and maintenance of membrane composition and integrity, are some of the crucial functions of sterols in plants. Followed by their synthesis in the endoplasmic reticulum, the sterols accumulate in the plasma membrane. The concept of sterol trafficking in plant cell is not well understood. The oxysterol binding proteins are implicated in sterol transport in non-plant systems. In the study, the oxysterol binding proteins in Arabidopsis and rice are described and classified. The Arabidopsis genome encodes 12 oxysterol binding proteins-related proteins (ORPs) as compared to 6 oxysterol binding proteins (OSBPs/ORPs) in rice. The protein alignment studies reveal that amino acid sequences for oxysterol binding proteins are relatively well conserved in Arabidopsis and rice. The rice OSBPs are classified based on their phylogenetic relationship with Arabidopsis ORPs. The sequence LOGO built on LOC_Os03g16690 indicated presence of fingerprint region of amino acids “EQVSHHPP” for Arabidopsis and rice OSBPs/ORPs. The organization of pleckstrin homology domain is identified in several OSBPs/ORPs in Arabidopsis and rice. The Arabidopsis oligonucleotide array data is explored to understand the expression patterns of ORPs under 17 different experimental conditions. The analysis showed the expression of ORPs in Arabidopsis is necessarily under the control of biotic stress, chemical, elicitor, hormone, light intensity, abiotic stress, and temperature conditions. The linear mean signal values for Arabidopsis ORPs revealed their relative expression patterns in different developmental stages. The genes for ORP3C and ORP3B are highly expressed in all developmental stages that were analyzed. The present study thus indicates crucial functional role of the individual members of this gene family in different environmental stress conditions.     

Evolution study of the Baeyer–Villiger monooxygenases enzyme family: Functional importance of the highly conserved residues

Baeyer–Villiger monooxygenases (BVMOs) catalyze the transformation of linear and cyclic ketones into their corresponding esters and lactones by introducing an oxygen atom into a C–C bond. This bioreaction has numerous advantages compared to its chemical version; it does not induce the use of potentially harmful reagents (i.e., green chemistry) and displays significant better enantio- and regio-selectivity.     

基于核糖体DNA内转录间隔区ITS序列的广义蓼属及近缘属分子系统学研究

通过对广义蓼属及近缘属共32个代表种内转录间隔区ITS序列的分子系统学分析,尝试研究备受争议的广义蓼属及近缘属的物种族、属、组级的划分问题,结果显示,广义蓼属在系统发育树上并不能形成一个单系类群,这些物种共聚为3大支,分别对应春蓼族、蓼族及荞麦族,其中荞麦属与翅果蓼属形成了一支独立于春蓼族及蓼族之外的类群。在春蓼族中,冰岛蓼属与分叉蓼组形成一个单系类群。     

A Liquid Chromatography-Mass Spectrometry-based Approach to Characterize the Substrate Specificity of Mammalian Heparanase

Extracellular heparanase activity releases growth factors and angiogenic factors from heparan sulfate (HS) storage sites and alters the integrity of the extracellular matrix. These activities lead to a loss of normal cell matrix adherent junctions and correlate with invasive cellular phenotypes. Elevated expression of heparanase is associated with several human cancers and with vascular remodeling. Heparanase cleaves only a limited fraction of glucuronidic linkages in HS. There have been few investigations of the functional consequences of heparanase activity, largely due to the heterogeneity and complexity of HS. Here, we report a liquid chromatography-mass spectrometry (LC-MS)-based approach to profile the terminal structures created by heparanase digestion and reconstruct the heparanase cleavage sites from the products. Using this method, we demonstrate that heparanase cleaves at the non-reducing side of highly sulfated HS domains, exposing cryptic growth factor binding sites. This cleavage pattern is observed in HS from several tissue sources, regardless of overall sulfation degree, indicating a common recognition pattern. We further demonstrate that heparanase cleavage of HS chains leads to increased ability to support FGF2-dependent cell proliferation. These results suggest a new mechanism to explain how heparanase might potentiate the uncontrolled cell proliferation associated with cancer through its ability to activate nascent growth factor-promoting domains within HS.     

白鱀豚BDNF基因的扩增和序列分析

利用聚合酶链式反应,首次从白鱀豚基因组DNA 中扩增和克隆到脑源神经营养因子的编码区。在该段序列中含有一个长为747 bp 的开放阅读框,无内含子,编码一个由248 个氨基酸组成的蛋白质,预计分子量为27 953.7道尔顿。其中包括由18 个氨基酸残基组成的信号肽区,111 个氨基酸残基组成的前肽区及119 个氨基酸残基组成的成熟区。序列分析表明,白鱀豚脑源神经营养因子基因编码区的核苷酸序列与其它哺乳动物相似性超过90%,而与猪牛相似性相对较高（分别为95% 和94.7%）。氨基酸序列比较发现,白鱀豚BDNF 前体蛋白的氨基酸序列与其它哺乳动物具有94.5% ～99.5%的相似性,显示了极高的保守性。通过邻接法进行的系统发生分析中,鲸目和食肉目的物种分别聚为单系;与其它哺乳动物相比,鲸类与有蹄类的牛和猪的亲缘关系相对较近,这与鲸类和有蹄类之间具有相对较近的亲缘关系相符。
     

Comparative Genomics of the Lipid-body-membrane Proteins Oleosin,Caleosin and Steroleosin in Magnoliophyte, Lycophyte and Bryophyte

Lipid bodies store oils in the form of triacylglycerols. Oleosin, caleosin and steroleosin are unique proteins localized on the surface of lipid bodies in seed plants. This study has identified genes encoding lipid body proteins oleosin, caleosin and steroleosin in the genomes of five plants: Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Selaginella moellendorffii and Physcomitrella patens. The protein sequence alignment indicated that each oleosin protein contains a highly-conserved proline knot motif, and proline knob motif is well conserved in steroleosin proteins, while caleosin proteins possess the Dx[D/N]xDG-containing calcium-binding motifs. The identification of motifs (proline knot and knob) and conserved amino acids at active site was further supported by the sequence logos. The phylogenetic analysis revealed the presence of magnoliophyte-and bryophyte-specific subgroups. We analyzed the public microarray data for expression of oleosin, caleosin and steroleosin in Arabidopsis and rice during the vegetative and reproductive stages, or under abiotic stresses. Our results indicated that genes encoding oleosin, caleosin and steroleosin proteins were expressed predominantly in plant seeds. This work may facilitate better understanding of the members of lipid-body-membrane proteins in diverse organisms and their gene expression in model plants Arabidopsis and rice.     

Phylogenetic analysis of the genus Microbacterium based on 16S rRNA gene sequences

Abstract 16S rRNA gene (rDNA) studies of the six species of the genus Microbacterium, M. lacticum, M. laevaniformans, M. dextranolyticum, M. imperiale, M. arborescens and M. aurum , were performed and the primary structures were compared with those of 29 representative actinobacteria and related organisms. Phylogenetic analysis indicated that six species of the genus Microbacterium and representative four species of the genus Aureobacterium appear to be phylogenetically coherent as was suggested by Rainey et al., although the peptidoglycan types of these two genera are different (peptidoglycan type B1 or B2). Thus, the phylogenetical analyses revealed that members of actinobacteria with group B-peptidoglycan do not cluster according to their peptidoglycan types, but form compact cluster different from actinobacteria or actinomycetes with group A-peptidoglycan.     

Phylogenetic position of the parasitoid nanoflagellate Pirsonia inferred from nuclear-encoded small subunit ribosomal DNA and a description of Pseudopirsonia n. gen. and Pseudopirsonia mucosa (Drebes) comb. nov

Sequences of the nuclear encoded small subunit (SSU) rRNA were determined for Pirsonia diadema, P. guinardiae, P. punctigerae, P. verrucosa, P. mucosa and three newly isolated strains 99-1, 99-2, 99-S. Based on phylogenetic analysis all Pirsonia strains, except P. mucosa, clustered together in one clade, most closely related to Hyphochytrium catenoides within the group of stramenopiles. However, P. mucosa was most closely related to Cercomonas sp. SIC 7235 and Heteromita globosa and belongs to the heterogenic group of Cercozoa. In addition to the SSU rDNA sequences, P. mucosa differs from the stramenopile Pirsonia species in some characteristics and was therefore redescribed in this paper as Pseudopirsonia mucosa. The three newly isolated strains 99-1, 99-2, and 99-S differed by 28 bp in their SSU rDNA sequences from their closest neighbour P. diadema and only 1 to 3 bp among themselves. These base differences and a host range similar to P. formosa were sufficient to assign them as new strains of P. formosa.     

Phylogenetic analysis of the internal transcribed spacer region of Japanese Lilium species

 The DNA from 16 Lilium species and one variety endemic to or naturalized in Japan were obtained and their internal transcribed spacer regions of nuclear ribosomal DNA (nrDNA) were amplified by PCR and sequenced by cycle sequencing. Phylogenetic analysis of the ITS sequences supported the validity of Comber’s classification system. It has also provided molecular evidence for the transfer of Lilium dauricum to sect. Sinomartagon. The phylogenetic relationships revealed by ITS DNA analysis were supported by previously published crossability data. The molecular phylogeny of Japanese Lilium species was discussed with reference to the putative migration routes of these species. Received: 30 June 1998 / Accepted: 19 October 1998     

蛋白质折叠识别方法综述

蛋白质折叠识别算法是蛋白质三维结构预测的重要方法之一,该方法在生物科学的许多方面得到卓有成效的应用。在过去的十年中,我们见证了一系列基于不同计算方式的蛋白质折叠识别方法。在这些计算方法中,机器学习和序列谱-序列谱比对是两种在蛋白质折叠中应用较为广泛和有效的方法。除了计算方法的进展外,不断增大的蛋白质结构数据库也是蛋白质折叠识别的预测精度不断提高的一个重要因素。在这篇文章中,我们将简要地回顾蛋白质折叠中的先进算法。另外,我们也将讨论一些可能可以应用于改进蛋白质折叠算法的策略。     

Phylogenetic analysis of the species with awnless lemma in Roegneria (Poaceae,Triticeae) based on single copy of nuclear gene DMC1

To investigate the phylogenetic relationships among species with awnless lemmas in Roegneria and their related diploid genera, the possible genomic constitution and genome donor of species with awnless lemmas in Roegneria, phylogenetic analyses of disrupted meiotic cDNA (DMC1) sequences were investigated in this study. The results showed that: (1) Roegneria alashanica-1 grouped with the Y-type sequences and Roegneria alashanica-2 grouped with the St-type sequences, confirming that Roegneria alashanica has the StY genomes. (2) Roegneria grandis-1 grouped with the Y-type sequences and Roegneria grandis-2 grouped with the St-type sequences, confirming that Roegneria grandis has the St^gY genomes, where the St genome from R. grandis is different from the St genome but is homologous with the Y genome. (3) Two Roegneria elytrigioides sequences grouped with the St-type sequences, confirming that Roegneria elytrigioides has the St₁St₂ genomes and should therefore be classified as Pseudoroegneria elytrigioides. (4) We prefer the suggestion that the Y genome is closely related to the St genome, however, the data do not certify that the St and Y genomes have the same origin.     

蛋白质MOTIF（纹基）的搜索及库的构建

蛋白质ＭＯＴＩＦ识别方法是研究和预测蛋白质结构和功能的一种工具。本文用理化性质矩阵描述蛋白质的特征保守多肽,构建了一个包含两千多个ＭＯＴＩＦ的库。并编制了快速而灵敏的ＯＴＩＦ搜索软件。文中特别以３种重要而难辨别的ＭＯＴＩＦ作为例证。此３种ＭＯＴＩＦ是：在ＭＲＮＡ剪接和翻译中起关键作用的ＲＮＰＭＯＴＩＦ,用于研究甘油激酶缺损和非胰岛素糖尿病等人类遗传病机制的糖激酶ＭＯＴＩＦ,以及许多直核组织中媒介序     

Phylogenetic systematics of the genus Echinococcus (Cestoda: Taeniidae)

Echinococcosis is a serious helminthic zoonosis in humans, livestock and wildlife. The pathogenic organisms are members of the genus Echinococcus (Cestoda: Taeniidae). Life cycles of Echinococcus spp. are consistently dependent on predator–prey association between two obligate mammalian hosts. Carnivores (canids and felids) serve as definitive hosts for adult tapeworms and their herbivore prey (ungulates, rodents and lagomorphs) as intermediate hosts for metacestode larvae. Humans are involved as an accidental host for metacestode infections. The metacestodes develop in various internal organs, particularly in liver and lungs. Each metacestode of Echinococcus spp. has an organotropism and a characteristic form known as an unilocular (cystic), alveolar or polycystic hydatid. Recent molecular phylogenetic studies have demonstrated that the type species, Echinococcus granulosus, causing cystic echinococcosis is a cryptic species complex. Therefore, the orthodox taxonomy of Echinococcus established from morphological criteria has been revised from the standpoint of phylogenetic systematics. Nine valid species including newly resurrected taxa are recognised as a result of the revision. This review summarises the recent advances in the phylogenetic systematics of Echinococcus, together with the historical backgrounds and molecular epidemiological aspects of each species. A new phylogenetic tree inferred from the mitochondrial genomes of all valid Echinococcus spp. is also presented. The taxonomic nomenclature for Echinococcus oligarthrus is shown to be incorrect and this name should be replaced with Echinococcus oligarthra.     

Phylogenetic analysis of the genus Aquaspirillum based on 16S rRNA gene sequences

Phylogenetic analysis of 15 species of the genus Aquaspirillum based on 16S rRNA gene (rDNA) sequences indicated that the genus Aquaspirillum is phylogenetically heterogeneous and the species could be divided into four groups as follows: Aquaspirillum serpens, the type species of this genus, A. dispar and A. putridiconchylium are situated in the family Neisseriaceae; members of the second group, A. gracile, A. delicatum, A. anulus, A. giesbergeri, A. sinuosum, A. metamorphum and A. psychrophilum, are included in the family Comamonadaceae; the two members of the third group, A. arcticum and A. autotrophicum, are included in the family Oxalobacteriaceae; and members of the fourth group, A. polymorphum, A. peregrinum, and A. itersonii, are included in the alpha-subdivision of Proteobacteria. Thus, phylogenetic studies indicated that all the species excepting A. serpens, the type species, should be transferred to distinct genera.     

Phylogenetic relationships of Combretoideae (Combretaceae) inferred from plastid,nuclear gene and spacer sequences

Phylogenetic relationships of the subfamily Combretoideae (Combretaceae) were studied based on DNA sequences of nuclear ribosomal internal transcribed spacer (ITS) regions, the plastid rbcL gene and the intergenic spacer between the psaA and ycf3 genes (PY-IGS), including 16 species of eight genera within two traditional tribes of Combretoideae, and two species of the subfamily Strephonematoideae of Combretaceae as outgroups. Phylogenetic trees based on the three data sets (ITS, rbcL, and PY-IGS) were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Partition-homogeneity tests indicated that the three data sets and the combined data set are homogeneous. In the combined phylogenetic trees, all ingroup taxa are divided into two main clades, which correspond to the two tribes Laguncularieae and Combreteae. In the Laguncularieae clade, two mangrove genera, Lumnitzera and Laguncularia, are shown to be sister taxa. In the tribe Combreteae, two major clades can be classified: one includes three genera Quisqualis, Combretum and Calycopteris, within which the monophyly of the tribe Combreteae sensu Engler and Diels including Quisqualis and Combretum is strongly supported, and this monophyly is then sister to the monotypic genus Calycopteris; another major clade includes three genera Anogeissus, Terminalia and Conocarpus. There is no support for the monophyly of Terminalia as it forms a polytomy with Anogeissus. This clade is sister to Conocarpus. Electronic Publication     

Sequence variations in the large-subunit ribosomal RNA gene of ammonia (foraminifera,protozoa) and their evolutionary implications

An unusually high divergence was observed in the ribosomal RNA genes of a free-living population of foraminifera belonging to the genusAmmonia. The sequences of a large-subunit (LSU) rDNA expansion segment D1 and flanking regions were obtained from 20 specimens namedAmmonia sp. 1 andAmmonia sp. 2. The sequence divergence between the two species averages 14%. Within each species it ranges from 0.2% to 7.1% inAmmonia sp. 1 and from 0.7% to 2.3% inAmmonia sp. 2. We did not find two specimens having identical sequences. Moreover, in opposition to the generally acaepted view, rDNA sequence variations were also found within a single individual. The variations among several rDNA copies in a single specimen ofAmmonia may reach up to 4.9%. Most of the observed variations result from multiplication of CA or TA serial repeats occurring in two particularly variable regions. For single base changes, C-T transitions are most frequently observed. We discuss the evolution of expansion segments and their use for phylogenetic studies. Correspondence to: J. Pawlowski     

Heparanase plays a dual role in driving hepatocyte growth factor (HGF) signaling by enhancing HGF expression and activity

Hepatocyte growth factor (HGF) is a heparin-binding cytokine that enhances growth, motility, and angiogenesis of many tumor types, including multiple myeloma where it is often highly expressed. However, little is known regarding what controls HGF level and activity in these tumors. Evaluation of bone marrow biopsies from myeloma patients revealed a strong positive correlation between the levels of HGF and heparanase, an endoglucuronidase known to promote aggressive tumor behavior. In vitro, addition of recombinant heparanase to myeloma cells or transfection of myeloma cell lines with the cDNA for heparanase significantly increased tumor cell expression and secretion of biologically active HGF. Shed syndecan-1, whose levels in myeloma are also enhanced by heparanase expression, binds to secreted HGF. This syndecan-1-HGF complex is active as shown by its ability to stimulate paracrine signaling via c-Met, the cell surface receptor for HGF. Surprisingly, heparanase enzyme activity was not required for up-regulation of HGF expression by the tumor cells. This is in contrast to the heparanase-mediated enhanced syndecan-1 shedding, which does require activity of the enzyme. This suggests that two different functional domains within the heparanase enzyme (the enzyme active site and a separate site) contribute to events leading to enhanced HGF signaling. These findings demonstrate a novel mechanism driving the HGF pathway whereby heparanase stimulates an increase in both HGF expression and syndecan-1 shedding to enhance HGF signaling. This work also provides further mechanistic insight into the dynamic role of heparanase in driving aggressive tumor progression.     

羊轮状病毒NT株VP1基因的测序和分子进化分析

摘要：【目的】为了研究羊轮状病毒NT株VP1基因的遗传进化规律,【方法】根据GenBank中相关VP1基因的保守序列,设计合成引物,扩增NT株VP1基因并进行克隆测序和序列分析。【结果】 氨基酸序列比较表明NT株与其他毒株VP1基因的相似性为77.3%～98.4%,且氨基酸突变多发生在VP1蛋白的非功能区。VP1蛋白进化树表明NT株与牛轮状病毒处于同一进化分支,有较近的亲缘关系。结合26株具有代表性的轮状病毒,计算毒株间VP1基因的核苷酸和氨基酸进化距离,并对核苷酸的同义突变率（dS）和非同义突变率（dN）进行研究,发现dN/dS的比值小于1,说明同义替代是VP1基因在进化过程中的主要变异。【结论】本文首次对羊轮状病毒NT株进行了VP1基因的测序,并对VP1基因的进化距离和进化规律进行深入探讨。