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PubMedDate not supplied

Analysis of major ampullate silk cDNAs from two non-orb-weaving spiders.

Compared to other arthropods, spiders are unique in their use of silk throughout their life span and the extraordinary mechanical properties of the silk threads they produce. Studies on orb-weaving spider silk proteins have shown that silk proteins are composed of highly repetitive regions, characterized by alanine and glycine-rich units. We have isolated and sequenced four partial cDNA clones representing major ampullate spider silk gene transcripts from two non-orb weavers: three for Kukulcania hibernalis and one for Agelenopsis aperta. These cDNA sequences were compared to each other, as well as to the previously published orb-weaver silk gene sequences. The results indicate that the repeats encoding conserved amino acid motifs such as polyA and polyGA that are characteristic of some orb-weaving spider silks are also found in some of the cDNAs reported in this study. However, we also found other motifs such as polyGS and polyGV in the cDNA sequences from the two non-orb-weaving spiders. The amino acid composition of the silk gland extracts shows that alanine and glycine are the major components of the silk of these two non-orb weavers as is the case in orb-weaver silks. Sequence alignment shows that A. aperta's cDNA displays a C-terminal encoding region that is about 44% similar to the one present in N. clavipes's MaSp1 cDNA. In addition, as previously observed for spider silk sequences, the analysis of the codon usage for these four cDNAs demonstrates a bias for A or T in the wobble base position.

Amino Acid Sequence↗
PubMed1995

The sequence and conformation of human pancreatic procarboxypeptidase A2. cDNA cloning, sequence analysis, and three-dimensional model.

A full-length cDNA clone coding for human pancreatic preprocarboxypeptidase A2 has been isolated from a lambda gt 11 human pancreatic library. Expression clones were identified by specific interaction with antisera raised against the native protein. The open reading frame of the polynucleotide sequence is 1254 base pairs in length and encodes a protein of 417 amino acids. This cDNA includes a short leader signal peptide of 16 amino acids and a 94-amino acid-long activation segment. The amino acid sequence shows 89% identity to that of rat procarboxypeptidase A2, the only A2 form sequenced so far, and 64% identity to that of human procarboxypeptidase A1. The newly determined sequence was modeled to the three-dimensional crystal structures of both bovine carboxypeptidase A and porcine procarboxypeptidase A1 by a novel distance geometry approach. Biases in the modeling were avoided by relying exclusively on automatic procedures and by using random structures as starting points. Information taken from the known homologous structures refers only to the backbone since no explicit data describing the conformation of side chains were transferred. Ten structures of human carboxypeptidase A2 were determined on the basis of each of the two known crystal structures. The root-mean-square distance for the backbone atoms between the 10 structures and their mean for 237 selected residues is 0.7 A when starting from the bovine protein and 0.8 A for 251 selected residues when starting from the porcine protein. The 94 residue-long activation segment was also determined in the modeling based on the porcine zymogen; its structure is well defined but not its orientation with respect to the enzyme moiety. The model obtained for human procarboxypeptidase A2 is discussed with respect to the specificity and activation of the enzyme.

Amino Acid Sequence↗
PubMedDate not supplied

cDNA cloning, sequencing, and differential expression of a heart-type fatty acid-binding protein in the mummichog (Fundulus heteroclitus).

A heart fatty acid-binding protein (H-FABP) cDNA was isolated from the liver of the mummichog (Fundulus heteroclitus) and the complete cDNA sequence and predicted amino acid sequence was determined. This cDNA binds to a mRNA product of 0.95 kb with the highest level of RNA expression in the male liver, gills, and gonads. Exposure of mummichogs to the polycyclic aromatic hydrocarbon (PAH) pyrene significantly down-regulated H-FABP expression at the highest concentration. This study provides evidence that environmentally relevant toxicants can modulate H-FABP expression.

Amino Acid Sequence↗
PubMed2006

Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences in poplar.

As part of a genomics strategy to characterize inducible defences against insect herbivory in poplar, we developed a comprehensive suite of functional genomics resources including cDNA libraries, expressed sequence tags (ESTs) and a cDNA microarray platform. These resources are designed to complement the existing poplar genome sequence and poplar (Populus spp.) ESTs by focusing on herbivore- and elicitor-treated tissues and incorporating normalization methods to capture rare transcripts. From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139,007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385,000 publicly available Populus ESTs. Clustering and assembly of 107,519 3'-end ESTs resulted in 14,451 contigs and 20,560 singletons, altogether representing 35,011 putative unique transcripts, or potentially more than three-quarters of the predicted c. 45,000 genes in the poplar genome. Using this EST resource, we developed a cDNA microarray containing 15,496 unique genes, which was utilized to monitor gene expression in poplar leaves in response to herbivory by forest tent caterpillars (Malacosoma disstria). After 24 h of feeding, 1191 genes were classified as up-regulated, compared to only 537 down-regulated. Functional classification of this induced gene set revealed genes with roles in plant defence (e.g. endochitinases, Kunitz protease inhibitors), octadecanoid and ethylene signalling (e.g. lipoxygenase, allene oxide synthase, 1-aminocyclopropane-1-carboxylate oxidase), transport (e.g. ABC proteins, calreticulin), secondary metabolism [e.g. polyphenol oxidase, isoflavone reductase, (-)-germacrene D synthase] and transcriptional regulation [e.g. leucine-rich repeat transmembrane kinase, several transcription factor classes (zinc finger C3H type, AP2/EREBP, WRKY, bHLH)]. This study provides the first genome-scale approach to characterize insect-induced defences in a woody perennial providing a solid platform for functional investigation of plant-insect interactions in poplar.

Animals↗
PubMed1998

Isolation and characterization of a wound-inducible ribonuclease from Nicotiana glutinosa leaves.

A wound-inducible ribonuclease (RNase NW) was purified from leaves of Nicotiana glutinosa. The purified RNase NW has an optimum pH around 5 and 7, and its base specificity is suggested based on the relative rates of hydrolysis of homopolyribonucleotides to be a preference for guanine base. The complete amino acid sequence of RNase NW was deduced by a combination of protein and cDNA sequencings. The cDNA sequence includes the entire coding sequence for a polypeptide with 229 amino acids including a putative secretion signal peptide at the N-terminus composed of 25 amino acids. The amino acids identified by the protein chemical methods are unambiguously localized within the deduced amino acid sequence from the cDNA sequence. Comparison of the sequence of RNase NW with those of other known plant RNases showed that it was identical except for eight residues to that of N. alata RNase NE, which is present in the style and pollen under normal conditions and is induced in roots in response to phosphate starvation [Dodds et al., Plant. Mol. Biol., 31, 227-238 (1996)]. RNase NW shows considerable sequence similarity to other known RNases, sharing 57% to 84% identical residues. Northern blot analysis using an RNase NW cDNA fragment as a probe showed that the RNase NW transcript was not detected in leaves without wounding, but it was induced within 4 h after wounding and then gradually decreased during 20 h.

Amino Acid Sequence↗
PubMed1992

Molecular cloning and nucleotide sequence of cDNA encoding human muscle glycogen debranching enzyme.

cDNA comprising the entire length of the human muscle glycogen debranching enzyme was cloned and its nucleotide sequence determined. The debrancher mRNA includes a 4545-base pair coding region and a 2371-base pair 3'-nontranslated region. The calculated molecular mass of the debrancher protein derived from cDNA sequence is 172,614 daltons, consistent with the estimated size of purified protein (Mr 165,000 +/- 500). A partial amino acid sequence (13 internal tryptic peptides with a total of 213 residues) determined on peptides derived from purified porcine muscle debrancher protein confirmed the identity of the cDNA clone. Comparison of the amino acid sequence predicted from the human glycogen debrancher cDNA with the partial protein sequence of the porcine debrancher revealed a high degree (88%) of interspecies sequence identity. RNA blot analysis showed that debrancher mRNA in human muscle, lymphoblastoid cells, and in porcine muscle are all similar in size (approximately 7 kilobases). Two patients with inherited debrancher deficiency had a reduced level of debrancher mRNA, whereas two other patients had no detectable abnormality in RNA blots. The isolation of the debrancher cDNA and determination of its primary structure is an important step toward defining the structure-function relationship of this multifunctional enzyme and in understanding the molecular basis of the type III glycogen storage disease.

Amino Acid Sequence↗
PubMed1993

Cloning and expression of immunologically active recombinant Amb a V allergen of short ragweed (Ambrosia artemisiifolia) pollen.

We have cloned and sequenced Amb a V, an Ambrosia artemisiifolia (short ragweed) pollen allergen that has proved to be particularly useful in the genetic analysis of human immune responsiveness. The amino acid sequence deduced from the cloned cDNA sequence corresponds to the published sequence of the protein, except that the cDNA sequence encodes an extra 10 amino acids at the C-terminus. The expressed 55-residue protein is then presumably cleaved enzymatically at the C-terminal lysine found in the 45-residue protein isolated from the pollen. The cloning and sequencing of Amb a V genomic DNA confirmed the cDNA sequence and showed that the Amb a V gene has no introns. Recombinant Amb a V allergen, expressed in Escherichia coli, bound to IgG and IgE antibodies in all Amb a V-allergic individuals tested and inhibition studies demonstrated that the recombinant protein contains a subset of the antigenic epitopes found on native Amb a V. In addition, recombinant Amb a V released histamine efficiently from basophils from Amb a V-allergic patients. The recombinant Amb a V allergen and mutants of Amb a V should, therefore, be useful in studies of allergen epitopes in humans, as well as providing a diagnostic tool.

Allergens↗
PubMed1998

Endometriotic lesions synthesize and secrete a haptoglobin-like protein.

To explore the identity and possible function of endometriosis protein-I (ENDO-I), which is an acidic glycoprotein synthesized and secreted by endometriotic lesions, partial amino acid sequence and cDNA sequence were determined. Partially purified, de novo-synthesized rat endometriosis glycoproteins were separated by two-dimensional SDS-PAGE, transferred to polyvinyl difluoride membranes, and stained with Coomassie blue. Protein corresponding to the size and pI of ENDO-I was cut from the membranes and analyzed by automated Edman degradation. ENDO-I amino acid sequence analysis identified 15 residues that shared significant homology with the beta-chain of rat, mouse, and human haptoglobin (Hp) and human Hp-related protein. Western blot analyses using anti-Hp antibody demonstrated cross-reactivity with de novo-synthesized ENDO-I protein in endometriosis culture media. For nucleotide sequence analysis, poly A-enriched mRNA was isolated from rat endometriotic tissues. A gene-specific oligonucleotide primer was designed and used for 3' rapid amplification of cDNA ends (RACE). Automated sequencing of RACE cDNA fragments identified 859 base pairs, of which 858 were identical to rat Hp. Reverse transcription-polymerase chain reaction was used to demonstrate that ENDO-I transcripts are differentially expressed by endometriosis but not by uterine tissues. In the human, distinct subtypes of Hp as well as proteins sharing epitopes with Hp have been used to diagnose a variety of diseases; therefore, Hp-like ENDO-I may prove to be a nonsurgical diagnostic tool to assess endometriosis. Hepatic Hp, induced by acute-phase stimuli, modulates macrophage function and angiogenic activity. If ENDO-I possesses similar activities, it may be involved with anomalies of the immune system or the etiology and pathophysiology of endometriosis.

Amino Acid Sequence↗
PubMed1984

Isolation of human fibroblast catalase cDNA clones. Sequence of clones derived from spliced and unspliced mRNA.

We report the isolation and sequence of partial cDNA clones coding for human catalase. These clones were recovered from a human fibroblast cDNA library by screening with mixtures of oligonucleotide probes deduced from the amino acid sequence of human erythrocyte catalase. A comparison of their nucleotide sequence with the known protein sequence and mapping of homologous DNA sequences to the short arm of chromosome 11 in somatic cell hybrids confirmed that they coded for catalase. One of these clones contained a 462-base insertion interrupting the coding sequence with stop codons in all three reading frames. The 5' and 3' ends of the insertion correspond to the donor and acceptor consensus sequences of introns. Inspection of clones lacking the insertion confirm the location of the splice sites. We suggest this clone corresponds to the product of reverse transcription of an unspliced mRNA species. The catalase gene is the closest genetic marker mapped to Wilms tumor, one of the most prevalent of childhood cancers. Catalase cDNA probes will be useful to the examination of mitotic recombination in the etiology of this disease and may provide a useful starting point to the search for the putative Wilms tumor gene.

Amino Acid Sequence↗
PubMed1997

cDNA cloning, sequence analysis and expression of a mouse 44-kDa nuclear protein copurified with DNA repair factors for acid-depurinated DNA.

We purified a 44-kDa nuclear protein from salt-extract of permeable mouse ascites sarcoma cells in an effort to isolate factors involved in the repair of acid-depurinated DNA. It was copurified with a major AP endonuclease (APEX nuclease) by sequential column chromatography then further purified by sodium dodecyl sulphate-polyacrylamide gel electrophoresis as a possible DNA repair support factor. Its partial amino acid sequences were determined, and a cDNA clone for the protein was isolated from a mouse T-cell cDNA library using long degenerate oligonucleotide probes deduced from the amino acid sequence. The complete nucleotide sequence of the cDNA (1.7 kilobases) was determined. Northern hybridization using this cDNA detected two transcripts: 1.8 kb being the major one and 2.6 kb being the minor one. The complete amino acid sequence for the protein predicted from the nucleotide sequence of the cDNA indicates that the 44-kDa protein consists of 394 amino acids with a calculated molecular weight of 43,698. In tests performed thus far, the recombinant 44-kDa protein expressed in Escherichia coli has not expressed any repair-support activity. It remains to be analyzed whether the protein attains this activity after appropriate posttranslational modifications. Most parts of the 44-kDa protein cDNA and the deduced amino acid sequence were found to be identical to those of the protein p38-2G4, recently reported as a cell cycle-specifically modulated nuclear protein of 38kDa. The p38-2G4 may be a truncated form of the present 44-kDa protein.

Amino Acid Sequence↗
PubMed1991

A novel system for large-scale sequencing of cDNA by PCR amplification.

We have developed a method for constructing a library containing the 3' end fragment of cDNA for large-scale sequencing of cDNA clones. The average size of the insert was 270 bp. Cell lysates that carry plasmids having the cDNA insert were subjected to PCR amplification of the cDNA moiety and the products were subjected to sequencing analysis using an autosequencer. With this protocol, sample preparation became a non-limiting step, that allowed us to sequence as many samples as the autosequencer could handle.

Base Sequence↗
PubMed1989

Murine muscle-specific enolase: cDNA cloning, sequence, and developmental expression.

In vertebrates, the glycolytic enzyme enolase (EC 4.2.1.11) is present as homodimers and heterodimers formed from three distinct subunits of identical molecular weight, alpha, beta, and gamma. We report the cloning and sequencing of a cDNA encoding the beta subunit of murine muscle-specific enolase. The corresponding amino acid sequence shows greater than 80% homology with the beta subunit from chicken obtained by protein sequencing and with alpha and gamma subunits from rat and mouse deduced from cloned cDNAs. In contrast, there is no homology between the 3' untranslated regions of mouse alpha, beta, and gamma enolase mRNAs, which also differ greatly in length. The short 3' untranslated region of beta enolase mRNA accounts for its distinct length, 1600 bases. It is known that a progressive transition from alpha alpha to beta beta enolase occurs in developing skeletal muscle. We show that this transition mainly results from a differential regulation of alpha and beta mRNA levels. Analysis of myogenic cell lines shows that beta enolase gene is expressed at the myoblast stage. Moreover, transfection of premyogenic C3H10T1/2 cells with MyoD1 cDNA shows that the initial expression of beta transcripts occurs during the very first steps of the myogenic pathway, suggesting that it could be a marker event of myogenic lineage determination.

Actins↗
PubMed2001

The rat interleukin 10 receptor: cloning and sequencing of cDNA coding for the alpha-chain protein sequence, and demonstration by western blotting of expression in the rat brain.

cDNA coding for the alpha chain of the rat interleukin 10 (IL-10) receptor was amplified by polymerase chain reaction (PCR), cloned and sequenced. The nucleic acid coding sequence exhibited 88% and 68% homology with the mouse and human IL-10 receptor sequences, respectively. The translated protein exhibited 83% and 61% homology with the mouse and human IL-10 receptor proteins. Specific antibodies were raised to the extracellular domain of the rat IL-10 receptor expressed as a secreted protein in recombinant Drosophila S2 cells. Western blotting using these antibodies demonstrated the presence of the IL-10 receptor in five major regions of the rat brain (cortex, cerebellum, hippocampus, hypothalamus and pituitary), supporting a role for IL-10 as a central regulator of inflammation.

Amino Acid Sequence↗
PubMed1986

A universal oligonucleotide probe for acetylcholine receptor genes. Selection and sequencing of cDNA clones for the mouse muscle beta subunit.

A region of 25 nucleotides is highly conserved in genes coding for the alpha, beta, gamma, and delta subunits of the nicotinic acetylcholine receptor (AChR) of human, mouse, calf, chicken, and Torpedo. Based on this observation, a 2-fold degenerate oligonucleotide was synthesized and used as a probe to screen a cDNA library made from a mouse myogenic cell line. Clones coding for the beta, gamma, and delta subunits were identified by the probe. The protein sequence deduced from the beta subunit clones codes for a precursor polypeptide of 501 amino acids with a calculated molecular weight of 56,930 daltons, which includes a signal peptide of 23 amino acids. The protein sequence and structural features of the beta subunits of mouse, calf, and Torpedo are conserved. A clone coding for the mouse gamma subunit was isolated, and its identity was confirmed by alignment of its sequence to previously published cDNA sequences for the mouse and calf gamma subunits. The clone contained approximately 200 nucleotides more at its 3' end untranslated region than a mouse gamma clone recently described. Northern blot analysis, utilizing as probes these beta and gamma subunit cDNAs and previously characterized alpha and delta subunit cDNAs, shows that the steady-state levels of the four AChR mRNAs increase coordinately during terminal differentiation of cultured C2 and C2i mouse myoblasts. The increase in mRNA levels can account for the rise of cell surface receptors during myogenesis and suggests that the muscle AChR genes may be regulated during development by a common mechanism. Utilization of this oligonucleotide probe should prove useful for screening a variety of libraries made from different species and tissues which are known to express AChRs.

Amino Acid Sequence↗
PubMed2002

Mouse cytosolic acetyl-CoA hydrolase, a novel candidate for a key enzyme involved in fat metabolism: cDNA cloning, sequencing and functional expression.

A cytosolic acetyl-CoA hydrolase (CACH) cDNA has been isolated from mouse liver cDNA library and sequenced. Recombinant expression of the cDNA in insect cells resulted in overproduction of active acetyl-CoA hydrolyzing enzyme protein. The mouse CACH cDNA encoded a 556-amino-acid sequence that was 93.5% identical to rat CACH, suggesting a conserved role for this enzyme in the mammalian liver. Database searching shows no homology to other known proteins, but reveals homological cDNA sequences showing two single-nucleotide polymorphisms (SNPs) in the CACH coding region. The discovery of mouse CACH cDNA is an important step towards genetic studies on the functional analysis of this enzyme by gene-knockout and transgenic approaches.

Acetyl-CoA Hydrolase↗
PubMed2003

cDNA nucleotide sequence coding for stearoyl-CoA desaturase and its expression in the zebrafish (Danio rerio) embryo.

A cDNA sequence of stearoyl-CoA desaturase (SCD) was determined from zebrafish (Danio rerio) and compared to the corresponding genes in several teleosts. Zebrafish SCD cDNA has a size of 1,061 bp, encodes a polypeptide of 325 amino acids, and shares 88, 85, 84, and 83% similarities with tilapia (Oreochromis mossambicus), grass carp (Ctenopharyngodon idella), common carp (Cyprinus carpio), and milkfish (Chanos chanos), respectively. This 1,061 bp sequence specifies a protein that, in common with other fatty acid desaturases, contains three histidine boxes, believed to be involved in catalysis. These observations suggested that SCD genes are highly conserved. In addition, an oligonucleotide probe complementary to zebrafish SCD mRNA was hybridized to mRNA of approximately 396 bases with Northern blot analysis. The Northern blot and RT-PCR analyses showed that the SCD mRNA was expressed predominantly in the liver, intestine, gill, and muscle, while a lower level was found in the brain. Furthermore, we utilized whole-mount in situ hybridization and real-time quantitative RT-PCR to identify expression of the zebrafish SCD gene at five different stages of development. This revealed that very high levels of transcripts were found in zebrafish at all stages during embryogenesis and early development.

Amino Acid Sequence↗