Nitric oxide synthase sequences in the marine fish Stenotomus chrysops and the sea urchin Arbacia punctulata, and phylogenetic analysis of nitric oxide synthase calmodulin-binding domains

The phylogenetic distribution and structural diversity of the nitric oxide synthases (NOS) remain important and issues that are little understood. We present sequence information, as well as phylogenetic analysis, for three NOS cDNAs identified in two non-mammalian species: the vertebrate marine teleost fish Stenotomus chrysops (scup) and the invertebrate echinoderm Arbacia punctulata (sea urchin). Partial gene sequences containing the well-conserved calmodulin (CaM)-binding domain were amplified by RT-PCR. Identical 375-bp cDNAs were amplified from scup brain, heart, liver and spleen; this sequence shares 82% nucleic acid and 91% predicted amino acid identity with the corresponding region of human neuronal NOS. A 387-bp cDNA was amplified from sea urchin ovary and testes; this sequence shares 72% nucleic acid identity and 65% deduced amino acid identity with human neuronal NOS. A second cDNA of 381 bp was amplified from sea urchin ovary and it shares 66% nucleic acid and 57% deduced amino acid identity with the first sea urchin sequence. Together with earlier reports of neuronal and inducible NOS sequences in fish, these data indicate that multiple NOS isoforms exist in non-mammalian species. Phylogenetic analysis of these sequences confirms the conserved nature of NOS, particularly of the calmodulin-binding domains.     

Bovine and feline gastrin cDNA sequences and the amino acid and nucleotide sequence homologies among mammalian species.

The complete nucleotide sequences of cDNAs encoding bovine and feline preprogastrins have been cloned from the antral mucosa mRNA. The gastrin mRNA of each animal encodes a preprogastrin of 104 amino acids consisting of a signal peptide, a prosegment of 37 amino acids, and a gastrin 34 sequence, followed by a glycine (the amide donor). The cleavage following a pair of lysine residues yields gastrin 17. We found that pairs of arginine residues flanking gastrin 34, the typical processing site sequence of all other preprogastrins and many peptide hormones, were arginines in the bovine preprogastrin, but the first basic amino acid pair had changed to Arg-Trp (57-58 residues) instead of Arg-Arg in the feline preprogastrin. Comparison of these amino acid and nucleotide sequences with published mammalian sequences showed extensive homology in the coding (63 to 73% amino acid identity) and in the untranslated regions (67 to 89% identity). Prosequence, the most variable region, shows greater amino acid difference between bovine and human preprogastrin (54% identity), and between bovine and rat preprogastrin (54% identity) than between other species (62 to 82% identity).     

草鱼呼肠孤病毒HZ08株S4基因序列分析

草鱼呼肠孤病毒HZ08株是本实验室从患出血病草鱼体内分离到的一个新毒株,已完成部分基因序列的分析,其氨基酸序列的同源性和873株相比,仅为20%~30%之间.因序列差异较大,无法通过设计特异性引物来扩增和分析其基因序列,采用单引物扩增技术,对HZ08株S4基因进行序列分析表明:S4全长为2263 bp,最大的ORF编码717个氨基酸,推导出其表达的蛋白约为79 kDa.正如其他基因节段,基因末端也含有保守碱基序列5′(GUAAUUU…UUCAUC),3′.S4基因推导的氨基酸序列与同宿主的其他呼肠孤病毒的非结构蛋白NS1同源性最大,其次是和哺乳动物正呼肠孤病毒的非结构蛋白mu-NS以及禽呼肠孤病毒非结构蛋白NS1同源性较大,表明S4可能表达细胞骨架相关蛋白.基于S4推导出的氨基酸序列构建的系统进化树HZ08株单独作为一个分支,与同宿主的其他呼肠孤病毒亲缘关系比较近,而与其他呼肠孤病毒则相对较远.这提示HZ08株可能是多个毒株的遗传信息经长期的遗传进化而得,综合其它已知序列信息,推测HZ08株可能为呼肠孤病毒的一个新成员.     

Purple acid phosphatases from bacteria: similarities to mammalian and plant enzymes

Mammalian and plant purple acid phosphatases have similar active site structures despite low sequence identity (<20%). Although no bacterial enzyme has been purified, a sequence database search revealed that genes that could encode potential purple acid phosphatases may be restricted to a small number of organisms (i.e. myco- and cyanobacteria). Analysis of their deduced amino acid sequences and predicted secondary structures indicates that the cyanobacterial enzyme is similar to both the mammalian and the recently discovered low-molecular-weight plant purple acid phosphatases, while the mycobacterial enzyme is homologous to the fungal and high-molecular-weight plant purple acid phosphatases. Homology models indicate that both bacterial proteins appear to be similar to mammalian purple acid phosphatases in the immediate vicinity of the active site. It is likely that these enzymes act as Fenton-type catalysts in order to prevent damage caused by reactive oxygen species generated by invaded host cells (M. tuberculosis) or by the light-harvesting complex (Synechocystis sp.).     

The chicken vimentin gene. Nucleotide sequence, regulatory elements, and comparison to the hamster gene

Here we report the nucleotide sequence of the chicken vimentin gene and its deduced primary amino acid sequence. A comparison of this gene to other intermediate filament protein genes demonstrates that both exon size and position are strongly conserved features of this multigene family. In addition, the hamster and chicken vimentin genes exhibit strong identity at the level of nucleotide (74%) and amino acid (80%) sequence. Interestingly, 40% of total sequence diversity is localized to the N terminus or "head" region of these genes whereas other protein domains (rod and C terminus) are remarkably identical in both nucleotide (81%) and amino acid (89%) sequence. Even stronger amino acid identity (100%) is exhibited in certain subdomains which may define regions crucial for filament formation and function. Not surprisingly, vimentin is more homologous across animal species than it is to other intermediate filament protein members (e.g. desmin) within the same species. A comparison of 5'-flanking sequences of the hamster and chicken genes as well as other characterized promoter elements (SV40, HSV-TK) reveals homologous sequence elements which may define common and/or unique sites involved in the modulation of gene expression. The implications of these sequence elements for both tissue-specific and developmental expression of the vimentin gene are discussed.     

Plant O-methyltransferases: molecular analysis,common signature and classification

Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32–71% sequence identity, and can be grouped according to the different compounds they utilise as substrates. Five highly conserved regions are proposed as a signature for plant O-methyltransferases, two of which (regions I and IV) are believed to be involved in S-adenosyl-L-methionine and metal binding, respectively. The glycine-rich signature regions include a 36 amino acid domain which is located in the mid-terminal section of the carboxy terminus of most O-methyltransferase sequences. Cladistic analysis of the amino acid sequences suggests that plant O-methyltransferases may have arisen from common ancestral genes that were driven by different structural and/or functional requirements, and whose descendants segregated into different biochemical species. A comprehensive classification of plant O-methyltransferases is proposed following the guidelines of the Commission of Plant Gene Nomenclature.     

Evolution of prothrombin: Isolation and characterization of the cDNAs encoding chicken and hagfish prothrombin

The cDNA sequences of chicken and hagfish prothrombin have been determined. The sequences predict that prothrombin from both species is synthesized as a prepro-protein consisting of a putative Gla domain, two kringle domains, and a two-chain protease domain. Chicken and hagfish prothrombin share 51.6% amino acid sequence identity (313/627 residues). Both chicken and hagfish prothrombin are structurally very similar to human, bovine, rat, and mouse prothrombin and all six species share 41% amino acid sequence identity. Amino acid sequence alignments of human, bovine, rat, mouse, chicken, and hagfish prothrombin suggest that the thrombin B-chain and the propeptide-Gla domain are the regions most constrained for the common function(s) of vertebrate prothrombins.The nucleotide sequences reported in this paper have been submitted to the EMBL/Genbank database under the following secession numbers: M 81391 for Gallus gallus, M 81393 for Eptatretus stouti.Correspondence to: R.T.A. MacGillivray     

Molecular cloning and characterization of alpha-class glutathione S-transferase genes from the hepatopancreas of red sea bream, Pagrus major

Two distinct cDNAs corresponding to GSTA1 and GSTA2 genes encoding glutathione S-transferases (GSTs) from the hepatopancreas of red sea bream, Pagrus major were cloned and sequenced. A comparison of the nucleotide sequences of GSTA1 and GSTA2 revealed 98% identity and their derived amino acid sequences had 96% similarity. Both genes could be classified as alpha-class GSTs on the basis of their amino acid sequence identity with other species. Genomic DNA cloning showed that both GSTA1 and GSTA2 genes consisted of six exons and five introns. In a comparison of genomic DNAs, the structures of GSTA1 and GSTA2 differed. In addition, Southern-blot analysis indicated that at least two kinds of alpha-class GSTs existed in the P. major genome. In order to biochemically characterize the recombinant enzymes (pmGSTA1-1 and pmGSTA2-2), both clones were highly expressed in Escherichia coli. The purified pmGSTA1-1 and pmGSTA2-2 exhibited glutathione conjugating activity toward 1-chloro-2,4-dinitrobenzene and glutathione peroxidase activity toward cumene hydroperoxide, while neither pmGSTs show detectable activity toward 1,2-dichloro-4-nitrobenzene, ethacrynic acid, 4-hydroxynonenal, or p-nitrobenzyl chloride. Despite their high level of amino acid sequence identity, the pmGSTs had quite different enzyme-kinetic parameters.     

Comparison of the Amino Acid Sequence and Phylogenetic Analysis of the Peplomer,Integral Membrane and Nucleocapsid Proteins of Feline,Canine and Porcine Coronaviruses

Complete nucleotide sequences were determined by cDNA cloning of peplomer (S), integral membrane (M) and nucleocapsid (N) genes of feline infectious peritonitis virus (FIPV) type I strain KU-2, UCD1 and Black, and feline enteric coronavirus (FECV) type II strain 79–1683. Only M and N genes were analyzed in strain KU-2 and strain 79–1683, which still had unknown nucleotide sequences. Deduced amino acid sequences of S, M and N proteins were compared in a total of 7 strains of coronaviruses, which included FIPV type II strain 79–1146, canine coronavirus (CCV) strain Insavc-1 and transmissible gastroenteritis virus of swine (TGEV) strain Purdue. Comparison of deduced amino acid sequences of M and N proteins revealed that both M and N proteins had an identity of at least 90% between FIPV type I and type II. The phylogenetic tree of the M and N protein-deduced amino acid sequences showed that FIPV type I and type II form a group with FECV type II, and that these viruses were evolutionarily distant from CCV and TGEV. On the other hand, when the S protein-deduced amino acid sequences was compared, identity of only about 45% was found between FIPV type I and type II. The phylogenetic tree of the S protein-deduced amino acid sequences indicated that three strains of FIPV type I form a group, and that it is a very long distance from the FIPV type II, FECV type II, CCV and TGEV groups.     

Xenopus laevis integrins. Structural conservation and evolutionary divergence of integrin beta subunits

We report the sequences of cDNA clones for two different integrin beta subunits isolated from a Xenopus laevis neurula cDNA library. mRNAs corresponding to both genes are first detected at gastrulation. We show that these two beta subunits are very highly related (98% identity in amino acid sequence) and probably arose at the time of tetraploidization of the X. laevis genome around 50 million years ago. Comparison of these sequences with those of various other vertebrate integrin beta subunit establishes that all species analyzed to date contain a highly conserved integrin beta subunit (beta 1). The interspecies homologies within this class of integrin beta subunits (82-86% identity in amino acid sequence) are much greater than those among the three different beta subunits which are known in humans (40-48% identity in amino acid sequence). Analysis of the homologies clearly indicates duplication and divergence of this multigene family more than 500 million years ago prior to the appearance of the vertebrates. We also observe cross-hybridization between cDNA probes for chicken integrin beta subunits and genomic DNAs of several invertebrate species. Despite the divergence in sequence among different integrin beta subunits, certain features of their structure are remarkably conserved.     

Molecular cloning of HSP70 in Mycoplasma ovipneumoniae and comparison with that of other mycoplasmas

Mycoplasma ovipneumoniae, a bacterial species that specifically affects ovine and goat, is the cause of ovine infectious pleuropneumonia. We cloned, sequenced and analyzed heat shock protein 70 (HSP70) (dnaK) gene of M. ovipneumoniae. The full length open reading frame of the M. ovipneumoniae HSP70 gene consists of 1812 nucleotides, with a G+C content of 34.16%, encoding 604 amino acids. Comparative analysis with the HSP70 sequences of 15 Mycoplasma species revealed 59 to 87% DNA sequence identity, with an amino acid sequence identity range of 58 to 94%. M. ovipneumoniae and M. hyopneumoniae shared the highest DNA and amino acid sequence identity (87 and 94%, respectively). Based on phylogenetic analysis, both the DNA and amino acid identities of M. ovipneumoniae with other mycoplasmal HSP70 were correlated with the degree of relationship between the species. The C-terminus of the HSP70 was cloned into a bacterial expression vector and expressed in Escherichia coli cells. The recombinant C-terminal portion of HSP70 protein strongly reacted with convalescent sera from M. ovipneumoniae-infected sheep, based on an immunoblotting assay. This indicates that HSP70 is immunogenic in a natural M. ovipneumoniae infection and may be a relevant antigen for vaccine development.     

A cross-species analysis of the cystic fibrosis transmembrane conductance regulator. Potential functional domains and regulatory sites.

To help elucidate the function of the cystic fibrosis transmembrane conductance regulator (CFTR), we have undertaken a cross-species analysis of the DNA sequence which encodes this protein. We have isolated and characterized the cDNA of the bovine homologue of CFTR. The deduced amino acid sequence shows high overall identity with the published sequences from human and mouse, although there is marked variability between the different potential functional domains. The region around human amino acid 508, which is deleted in 70% of cystic fibrosis chromosomes, is highly conserved across species; of the missense cystic fibrosis mutations reported to date, all of the amino acids in the normal human sequence are conserved in the bovine and mouse sequences. A single amino acid encoded by the human cDNA (Ser-434) is missing in the bovine sequence, and there are two amino acids encoded by the bovine sequence which are absent in the human. These all stem from in-frame 3-base omissions within the sequences. In addition to the cow, we amplified the DNA sequences encoding a portion of the R-domain from sheep, monkey, rabbit, and guinea pig. These sequences show relatively low overall sequence identity (63%), but nearly all of the potential protein kinase A and protein kinase C phosphorylation sites are conserved over all of the species examined. Our results suggest functional significance for certain highly conserved residues and putative domains within CFTR.     

gamma-Tubulin in Arabidopsis: gene sequence, immunoblot, and immunofluorescence studies.

gamma-Tubulin is a protein associated with microtubule (Mt)-organizing centers in a variety of eukaryotic cells. Unfortunately, little is known about such centers in plants. Genomic and partial cDNA clones encoding two gamma-tubulins of Arabidopsis were isolated and sequenced. Comparisons of genomic and cDNA sequences showed that both genes, TubG1 and TubG2, contain nine introns at conserved locations. The sequences of the two genes both predict proteins containing 474 amino acids, with molecular masses of 53,250 and 53,280 D, respectively. The predicted gamma 1- and gamma 2-tubulins exhibit 98% amino acid identity with each other and approximately 70% amino acid identity with the gamma-tubulins of animals and fungi. RNA gel blot results demonstrated that both genes are transcribed in suspension culture cells, seedlings, and roots and flowers of mature plants. Immunoblots of Arabidopsis proteins using an antibody specific to a conserved peptide of gamma-tubulin showed a major cross-reacting polypeptide with an M(r) of 58,000. The same antibody stained all Mt arrays in tissue and suspension culture cells of this species. Binding was inhibited by the homologous oligopeptide in the gamma-tubulins predicted by the two Arabidopsis gene sequences. Antibody staining avoided the plus ends of Mts at the kinetochores and cell plate, but unlike the case in animal cells, seemed to be localized over broad stretches of the kinetochore fibers and phragmoplast toward the minus ends. We concluded that at least two gamma-tubulin protein homologs are present in Arabidopsis and that at least one of them is localized along Mt arrays. Its distribution is correlated with and may help explain unique characteristics of Mt organization in plants.     

Evolutionary and structural relationships among the group-specific component, albumin and alpha-fetoprotein.

The group-specific component (Gc) is a plasma protein that binds vitamin D. Recent characterization of human Gc cDNA demonstrated homology with serum albumin and alpha-fetoprotein. This study compares the sequences of the three proteins and demonstrates a strong evolutionary relationship. Albumin, alpha-fetoprotein and Gc evolved from an ancestral gene containing an intragenic triplication. Comparison of the amino acid sequences and patterns of double disulfide bonds suggests that the Gc gene may have diverged from an ancestral gene earlier in evolution than the genes encoding albumin and alpha-fetoprotein. Analysis of the amino acid and nucleotide sequences of the three internal domains of Gc revealed 19-23% amino acid sequence identity and the localization of three homology blocks with 40-44% nucleotide sequence identity. The deduced amino sequence of Gc furnished data for comparing its molecular configuration based on the predicted secondary structure with those predicted for human albumin and alpha-fetoprotein. Utilization of Gc cDNA has also led to the identification of its genomic DNA and detection of a human DNA polymorphism.     

副粘病毒Tianjin株NP、P、M及L蛋白的生物信息学分析

为了进一步明确副粘病毒Tianjin株的来源和种系进化地位,探讨其高致病性的机制.对Tianjin株NP、P、M及L蛋白进行了生物信息学分析.进化树显示:Tianjin株属于副粘病毒亚科呼吸道病毒属,且很可能为仙台病毒新的基因型.相似性比较表明,P蛋白变异最大.相似性仅为78.7%～91.9%;L蛋白相似性最高,为96.0%～98.0%.序列比对显示:NP蛋白氨基酸序列中存在15个独特的变异位点,P蛋白存在29个,M蛋白存在6个,L蛋白存在29个.这些独特变异位点的存在很可能是导致Tianjin株在宿主来源和致病特点等方面与已知仙台病毒株具有较大差异的原因.     

A cytochrome P4501B gene from a fish, Pleuronectes platessa

Tetrapod cytochrome P4501 family (CYP1A1, CYP1A2 and CYP1B1) enzymes are most active in hydroxylating a variety of environmental contaminants including polyaromatic hydrocarbons (PAH), planar polychlorinated biphenyls and arylamines and thus play a pivotal role in the toxicology of these compounds. Mammalian CYP1A1 and CYP1A2 genes appear to have diverged after the evolutionary emergence of mammals, whereas fish species apparently possess only one CYP1A family gene, and fish CYP1A enzymes exhibit properties of both of the mammalian isoforms. We have isolated a further CYP1 family gene from a marine flatfish (plaice; Pleuronectes platessa), which, on the basis of exon organisation and sequence similarity, can be assigned as a piscine CYP1B. Its deduced amino acid sequence shows the closest (54%) identity to mammalian CYP1B1 proteins and, on the basis of molecular modeling studies, shows a high degree of positional and structural conservation of the substrate contacting amino acid residues in its putative active site when compared to other CYP1 enzymes. Phylogenetic analysis of fish and mammalian CYP1 family sequences indicates that the plaice CYP1B and mammalian CYP1B1 genes share a common ancestry. Plaice CYP1B has a more restricted tissue expression profile than the previously isolated plaice CYP1A, only being detectable, by Northern blotting, in gill tissue. In contrast to CYP1A, which shows extensive PAH-dependent induction in a variety of tissues, plaice CYP1B appears unresponsive to treatment with a prototypical PAH-type inducer, beta-naphthoflavone (BNF).