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At least 1,099 records · Page 61Linked to original sources
PubMed1988

cDNA sequence encoding the 16-kDa proteolipid of chromaffin granules implies gene duplication in the evolution of H+-ATPases.

Vacuolar H+-ATPases function in generating protonmotive force across the membranes of organelles connected with the vacuolar system of eukaryotic cells. This family of H+-ATPases is distinct from the two other families of H+-ATPases, the plasma membrane-type and the eubacterial-type. One of the subunits of the vacuolar H+-ATPase binds N,N'-dicyclohexylcarbodiimide (DCCD) and has been implicated in the proton-conducting activity of these enzymes. We have cloned and sequenced the gene encoding the DCCD-binding protein (proteolipid) of the H+-ATPase of bovine chromaffin granules. The gene encodes a highly hydrophobic protein of 15,849 Da. Hydropathy plots revealed four transmembrane segments, one of which contains a glutamic residue that is the likely candidate for the DCCD binding site. Sequence homology with the vacuolar proteolipid and with the proteolipids of eubacterial-type H+-ATPases was detected. The proteolipids from Escherichia coli, spinach chloroplasts, and yeast mitochondria matched better to the NH2-terminal part of the vacuolar protein. The proteolipids of bovine mitochondria and Neurospora mitochondria matched better to the COOH-terminal end of the vacuolar proteolipid. These findings suggest that the proteolipids of the vacuolar H+-ATPases were evolved in parallel with the eubacterial proteolipid, from a common ancestral gene that underwent gene duplication.

Amino Acid Sequence↗
PubMed1994

Evolutionary relationships of lactate dehydrogenases (LDHs) from mammals, birds, an amphibian, fish, barley, and bacteria: LDH cDNA sequences from Xenopus, pig, and rat.

The nucleotide sequences of the cDNAs encoding LDH (EC 1.1.1.27) subunits LDH-A (muscle), LDH-B (liver), and LDH-C (oocyte) from Xenopus laevis, LDH-A (muscle) and LDH-B (heart) from pig, and LDH-B (heart) and LDH-C (testis) from rat were determined. These seven newly deduced amino acid sequences and 22 other published LDH sequences, and three unpublished fish LDH-A sequences kindly provided by G. N. Somero and D. A. Powers, were used to construct the most parsimonious phylogenetic tree of these 32 LDH subunits from mammals, birds, an amphibian, fish, barley, and bacteria. There have been at least six LDH gene duplications among the vertebrates. The Xenopus LDH-A, LDH-B, and LDH-C subunits are most closely related to each other and then are more closely related to vertebrate LDH-B than LDH-A. Three fish LDH-As, as well as a single LDH of lamprey, also seem to be more related to vertebrate LDH-B than to land vertebrate LDH-A. The mammalian LDH-C (testis) subunit appears to have diverged very early, prior to the divergence of vertebrate LDH-A and LDH-B subunits, as reported previously.

Amino Acid Sequence↗
PubMed1998

Analysis of xylem formation in pine by cDNA sequencing.

Secondary xylem (wood) formation is likely to involve some genes expressed rarely or not at all in herbaceous plants. Moreover, environmental and developmental stimuli influence secondary xylem differentiation, producing morphological and chemical changes in wood. To increase our understanding of xylem formation, and to provide material for comparative analysis of gymnosperm and angiosperm sequences, ESTs were obtained from immature xylem of loblolly pine (Pinus taeda L.). A total of 1,097 single-pass sequences were obtained from 5' ends of cDNAs made from gravistimulated tissue from bent trees. Cluster analysis detected 107 groups of similar sequences, ranging in size from 2 to 20 sequences. A total of 361 sequences fell into these groups, whereas 736 sequences were unique. About 55% of the pine EST sequences show similarity to previously described sequences in public databases. About 10% of the recognized genes encode factors involved in cell wall formation. Sequences similar to cell wall proteins, most known lignin biosynthetic enzymes, and several enzymes of carbohydrate metabolism were found. A number of putative regulatory proteins also are represented. Expression patterns of several of these genes were studied in various tissues and organs of pine. Sequencing novel genes expressed during xylem formation will provide a powerful means of identifying mechanisms controlling this important differentiation pathway.

DNA, Complementary↗
PubMed1996

Gene structure and cDNA sequence identify the beaded filament protein CP49 as a highly divergent type I intermediate filament protein.

The fiber cell of the vertebrate ocular lens assembles a cytoskeletal structure, the beaded filament, which contains two proteins unique to the fiber cell: CP49 (phakinin) and CP115/CP95 (filensin). We report here the complete primary sequence and gene structure for human CP49. These data show that CP49 is a member of the intermediate filament family, but highly unusual in several regards. 1) CP49 primary sequence does not permit unambiguous assignment to any existing class of intermediate filament protein, but exhibits a gene structure that is identical to the Type I cytokeratins. 2) CP49 essentially lacks one of the three major domains that characterize all intermediate filament proteins, the carboxyl-terminal tail domain. 3) CP49 shows substitutions at 3 of 4 residues in the otherwise highly conserved intermediate filament protein motif LNDR. Notably, this divergence includes an Arg to Cys substitution that has only been observed in the mutant human cytokeratin K14, a mutation shown to cause the skin blistering seen in the genetic disorder Dowling-Meara epidermolysis bullosa simplex.

Amino Acid Sequence↗
PubMed1997

The complete cDNA sequence and structural polymorphism of the polypeptide chain of porcine submaxillary mucin.

The complete structure of the DNA encoding the polypeptide chain of porcine submaxillary mucin has been determined. The polypeptide is composed of distinct domains. A large central domain containing tandem repeats of 81 residues each is flanked by much shorter domains with sequences similar to the tandem repeats. Four disulfide-rich domains, three at the amino terminus and one at the carboxyl terminus, complete the chain. The disulfide-rich domains have significant sequence identity to those of other mucins and prepro-von Willebrand factor. The coding region of the mucin gene is highly polymorphic, and three alleles were identified in a single animal that encoded different numbers of the 81-residue tandem repeats. A single large exon devoid of introns encodes the tandem repeat domains. The largest allele with 135 tandem repeats encoded 13,288 amino acids to give a polypeptide with Mr = 1,184,106. The other two alleles contained 99 and 125 tandem repeats, respectively. Each allele also showed different restriction fragment length polymorphisms, which is consistent with the different patterns seen in individual animals. Fragment length polymorphism was also seen within two different families of animals, indicating that the polymorphism observed occurs in a single generation.

Alleles↗
PubMed2001

A novel family of chitin-binding proteins from insect type 2 peritrophic matrix. cDNA sequences, chitin binding activity, and cellular localization.

The peritrophic matrix is a prominent feature of the digestive tract of most insects, but its function, formation, and even its composition remain contentious. This matrix is a molecular sieve whose toughness and elasticity are generated by glycoproteins, proteoglycans, and chitin fibrils. We now describe a small, highly conserved protein, peritrophin-15, which is an abundant component of the larval peritrophic matrices of the Old World screwworm fly, Chrysomya bezziana, and sheep blowfly, Lucilia cuprina. Their deduced amino acid sequences code for a 8-kDa secreted protein characterized by a highly conserved and novel register of six cysteines. Two Drosophila homologues have also been identified from unannotated genomic sequences. Recombinant peritrophin-15 binds strongly and specifically to chitin; however, the stoichiometry of binding is low (1:10,000 N-acetyl glucosamine). We propose that peritrophin-15 caps the ends of the chitin polymer. Immunogold studies localized peritrophin-15 to the peritrophic matrix and specific vesicles in cells of the cardia, the small organ of the foregut responsible for peritrophic matrix synthesis. The vesicular contents are disgorged at the base of microvilli underlying the newly formed peritrophic matrix. This is the first time that the process of synthesis and integration of a peritrophic matrix protein into the nascent peritrophic matrix has been observed.

Amino Acid Sequence↗
PubMedDate not supplied

Expression and cDNA sequence of matrix metalloproteinase-2 (MMP-2) in a mammalian model of human disease processes: Tupaia belangeri.

Matrix metalloproteinase-2 (MMP-2) is one of a family of proteolytic enzymes that are involved in the remodelling of tissue during normal growth processes and is capable of degrading structural components of the extracellular matrix. Increases in MMP-2 expression and activity have been reported in diseases that involve degradation of the extracellular matrix. Reported here for the first time are the relative levels of expression of MMP-2 in tissues of the tree shrew along with 2587 bases of the mRNA sequence. Translation of this sequence predicts a protein 660 amino acids in length, containing all of the features expected of mammalian MMP-2. The tree shrew is a species close to the primate line and is an emerging animal model for a variety of human diseases, including hepatitis and myopia that feature MMP-2 mediated remodelling of the extracellular matrix.

Amino Acid Sequence↗
PubMed2005

Casein kinase 2 during early embryonic development in silkworm Bombyx mori: cDNA sequence, gene expression, and enzyme activity.

To clarify the property of casein kinase 2 (CK2) during early embryonic development in the silkworm, we compared the phosphorylation activities of CK2 in non-diapause and diapause eggs until 60 h after oviposition. In nondiapause eggs, the phosphorylated signals were found at each stage and became progressively stronger through each stage. On the other hand, in diapause eggs, the strongest phosphorylated signals were found at approximately 12 to 24 h after oviposition and became progressively weaker through each stage. To clarify the control mechanism of these enzyme activities, we tried to clone cDNAs encoding alpha- and beta-subunit of CK2 and analyze the gene expressions. The deduced amino acid sequence of the isolated cDNAs comprised 342 and 220 residues, and these sequences showed 85-90% identities to the alpha- and beta-subunit of CK2 in Spodoptera frugiperda. RT-PCR indicated that these genes were expressed in nondiapause and diapause eggs. However, these genes expressions were not parallel with the changes in CK2 activity. These results suggest that the changes in CK2 activity are regulated mainly at the level of post-transcription during embryonic development in Bombyx mori.

Amino Acid Sequence↗
PubMed2004

Analysis of cDNA sequences of feline SAAs.

Feline amyloidosis is an uncommon disorder caused by deposits of amyloid in a variety of organs. Most frequently encountered types are amyloid derived of pancreatic islet amyloid polypeptide (AIAPP) in older cats and of the apolipoprotein, apo-serum amyloid A (AA) in Abyssinian/Somali (Aby) and Siamese/Oriental (Siam) cats occurring at a relatively young age. For the AA protein of the Aby, Siam and domestic shorthair cat (DSH) breed different amino acid sequences have been described. It is not yet clear, however, whether the tendency to develop AA amyloidosis in Aby and Siam is associated with specific apoSAA protein sequences and whether this is breed specific. In this study, DNA from one Siam and two DSH cats revealed on Southern blot three bands suggesting at least three genes or gene clusters. The SAA cDNAs of hepatic mRNA from three Abys, five Siams and five DSHs were amplified by RT-PCR, cloned and sequenced. Siams and Abys had limited SAA sequence variability. All five Siams, three of which were positive for amyloid, had the amyloidogenic Siam SAA and the amyloidogenic Aby SAA sequence. Two of the Abys, both with amyloid, had the amyloidogenic Aby SAA sequence. The third Aby, without amyloid, missed its amyloidogenic sequence. The SAA sequences of the DSHs found in the present preliminary survey, suggested a possible tendency for more variability, whereas the amyloidogenic Siam as well as the amyloidogenic Aby sequence were found once. Up to five different sequences were found in a single animal. All five DSHs, moreover, had a specific sequence lacking in the Siams and Abys. The present results, especially those of the Siams, favor that in addition to the occurrence of amyloid associated SAA genes other factors such as infections and inflammatory processes are involved in the development of phenotypical amyloidosis.

Amino Acid Sequence↗
PubMed1996

cDNA sequence analysis of a novel cardiotoxin-like protein from Taiwan banded krait.

The cDNAs encoding a novel protein was constructed from the cellular RNA isolated from the venom glands of Bungarus multicinctus by reverse transcription-polymerase chain reaction. The deduced amino acid sequence of this novel protein contained 65 amino acid residues with 8 cysteine residues. Comparative sequence analysis showed that it was structurally related to cardiotoxin rather than neurotoxins. These results suggest that the venom of Bungarus multicinctus may contain cardiotoxin(s) which was not noticed before.

Amino Acid Sequence↗
PubMed1997

cDNA sequence analysis of cardiotoxin variants from Taiwan cobra.

Five cDNAs encoding cardiotoxin variants were constructed from the cellular RNA isolated from the venom glands of Naja naja atra by reverse transcription-polymerase chain reaction. A high degree of nucleotide sequence homology was observed between these variants and other determined ones. Among them, a novel cardiotoxin 6 had 61 amino acid residues rather than 60 ones that usually observed with Naja naja atra cardiotoxins. The other cardiotoxin variants were the homologues of cardiotoxins 1, V or N with one or two amino acid substitutions, respectively. These results probably reflect the involvement of RNA editing in the production of cardiotoxin variants in the venom of Taiwan cobra.

Amino Acid Sequence↗
PubMed2000

Preparation and cDNA sequence analysis of two novel monoclonal antibodies against magaininII.

By using intrasplenic immunization and the conventional B lymphocyte hybridoma technique, we have established two novel hybridoma cell lines stably secreting specific monoclonal antibodies (MAbs) to magaininII, termed as 2D1 and 3F8, respectively. The two cell lines were then subjected to RNA extraction and the VH and VL segments were obtained by reverse transcription of RNA followed by polymerase chain reaction (RT-PCR) and characterized by nucleotide sequence analysis. The VH segments of 2D1 and 3F8 belong to the VH5 family and the VL segments of 2D1 and 3F8 belong to VK10 and VK1 groups, respectively. The two MAbs utilize different VL segments and have disparities in their HCDR3 regions, which may contribute to the different epitope recognition of the two antibodies.

Amino Acid Sequence↗
PubMed1992

Complete human NF1 cDNA sequence: two alternatively spliced mRNAs and absence of expression in a neuroblastoma line.

Neurofibromatosis type 1 (NF1) is caused by mutations in a large gene on chromosome 17q11.2. Previously described partial cDNAs for this gene predicted a protein related to yeast IRA1/IRA2 and the mammalian RAS GTPase activator protein GAP. To initiate a detailed study of the role of this gene in NF1, we have characterized a set of overlapping cDNAs that represent its complete coding sequence. Our results show that two differentially expressed human NF1 mRNAs differ by a 63-bp insertion in the GAP-related domain. These mRNAs predict two 2,818- and 2,839-amino acid proteins with calculated molecular masses of approximately 317 and 319 kD. Extensive similarity to IRA proteins is evident in a 1,450-amino-acid central segment, roughly between amino acids 900 and 2,350. However, the remainder of the NF1 protein is not significantly similar to other proteins. Interestingly, the SK-N-SH human neuroblastoma line expresses no detectable NF1 mRNA, indicating that expression of NF1 is not essential for viability of this neural crest-derived tumor cell line.

Alternative Splicing↗
PubMed1999

cDNA sequence analysis of monoclonal antibody FU-MK-1 specific for a transmembrane carcinoma-associated antigen, and construction of a mouse/human chimeric antibody.

Mouse monoclonal antibody (MAb) FU-MK-1, raised against a human gastric adenocarcinoma, recognizes a transmembrane antigen, GA733-2, present on most adenocarcinomas and seems to be of potential utility for immunodiagnosis and immunotherapy of those cancers. However, an inherent problem in their in vivo application is the human anti-mouse antibody response. In this study, we cloned and sequenced the variable region genes of the heavy and light chains (V(H) and Vkappa) of FU-MK-1 using the reverse transcription-polymerase chain reaction method. Then, we constructed a mouse/human chimeric antibody, designated as Ch FU-MK-1, by fusing the FU-MK-1 V(H) and Vkappa genes to the human Cgamma1 and Ckappa genes, respectively, and by ligating the chimeric H and L chain genes to each other in a mammalian cell expression vector. The final gene construct was transfected into mouse non-Ig-producing hybridoma cells by electroporation. The Ch FU-MK-1 antibody thus prepared bound to human adenocarcinoma cells and competitively inhibited the binding of the parental FU-MK-1 to the adenocarcinoma cells. Ch FU-MK-1 also showed a potent antibody-dependent cell-mediated cytotoxicity (ADCC) with human peripheral blood mononuclear cells as effectors against the adenocarcinoma cells, indicating that this chimeric antibody seems to be suitable for in vivo therapeutic approaches.

Adenocarcinoma↗
PubMed2003

ESTprep: preprocessing cDNA sequence reads.

MOTIVATION: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases. RESULTS: This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank. AVAILABILITY: The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html

Algorithms↗
PubMed2000

Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing.

As a first step towards a more comprehensive functional characterization of cDNAs than bioinformatic analysis, which can only make functional predictions for about half of the cDNAs sequenced, we have developed and tested a strategy that allows their systematic and fast subcellular localization. We have used a novel cloning technology to rapidly generate N- and C-terminal green fluorescent protein fusions of cDNAs to examine the intracellular localizations of > 100 expressed fusion proteins in living cells. The entire analysis is suitable for automation, which will be important for scaling up throughput. For > 80% of these new proteins a clear intracellular localization to known structures or organelles could be determined. For the cDNAs where bioinformatic analyses were able to predict possible identities, the localization was able to support these predictions in 75% of cases. For those cDNAs where no homologies could be predicted, the localization data represent the first information.

Animals↗