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PubMed2006

The cDNA sequencing project.

The Dictyostelium discoideum cDNA sequencing project started in 1995, preceding the genome sequencing project. Altogether, 14 cDNA libraries, including full-length ones, were constructed from five different stages of growth and asexual and sexual development, from which nearly 100,000 randomly chosen clones were sequenced to yield over 150,000 expressed sequence tags (ESTs). The data have been publicized online to facilitate clone distribution and collaboration using the whole clone set for microarray analyses. The EST reads were assembled to 6700 independent genes, which constitute about 55% of the total estimated Dictyostelium genes. Utilization of wet and dry resources have contributed to the understanding of the genetic system controlling the multicellular development in Dictyostelium.

Animals↗
PubMedDate not supplied

Concatenation cDNA sequencing for transcriptome analysis.

We describe a high-throughput cDNA sequencing pipeline (http://www.hgsc.bcm.tmc.edu/projects/cdna) built in response to the emerging need for rapid sequencing of large cDNA collections. Using this strategy cDNA inserts are purified and joined through concatenation into large molecules. These 'pseudo-BACs' are subjected to random shotgun sequencing whereby the majority of cDNA inserts in the pool are sequenced. Using this concatenation cDNA sequencing platform, we have contributed more than 13000 full-length cDNA sequences from human and mouse to the Mammalian Gene Collection (MGC).

Cloning, Molecular↗
PubMed1991

Hepatitis delta virus cDNA sequence from an acutely HBV-infected chimpanzee: sequence conservation in experimental animals.

Hepatitis delta virus (HDV) RNA was isolated from the serum of a chimpanzee acutely infected with hepatitis B virus (HBV) and superinfected with HDV. Interference of HDV with HBV resulted in decreased HBV DNA levels in the serum. This interference did not change the size of the two HBV specific RNAs present in the liver of the chimpanzee. The complete cDNA sequence of the HDV RNA (5th passage) was determined. Comparison of this cDNA sequence with our previously published sequence (4th passage), located in the variable domain of HDV, was highly conserved. The HDV strain used for these infections originated from a human HDV isolate also used for five to seven HDV passages in chronic HBV carrier chimpanzees (subtypes adw and ayw) or woodchucks chronically infected with woodchuck hepatitis virus (WHV). The complete HDV cDNA sequence showed an extreme conservation (up to 99.8% homology) with the previously published animal-derived HDV cDNA sequences irrespective of passage number and animal species. In contrast a markedly lower homology (85-89%) was found when compared with 3 human-derived HDV cDNA sequences. Comparison of our complete cDNA sequence with the human-derived cDNA sequences showed that the nucleotide changes in the human-derived isolates were restricted to specific regions on the genome and to specific basepair substitutions. The hepatitis Delta antigen (HDAg) is highly conserved both in the human- and animal-derived cDNA sequences showing mainly conservative amino acid changes.

Acute Disease↗
PubMed1986

Complete amino acid sequence of rat L-type pyruvate kinase deduced from the cDNA sequence.

cDNA clones, containing the entire coding region of rat L-type pyruvate kinase, were isolated and their nucleotide sequences were determined by the dideoxy-chain-termination method. The predicted coding region, which spans 543 amino acids, established the complete amino acid sequence of the L-type isozyme of pyruvate kinase for the first time. The deduced amino acid sequence of the L type has one phosphorylation site in its amino terminus and shows about 68% and 48% homologies with M1-type pyruvate kinase of chicken and yeast pyruvate kinase respectively. Domain A exhibits higher homology than domains B and C. The residues in the active site of the L-type enzyme of rats, lying between domains B and A2, are rather different from those of the M1-type enzyme of chickens, but other residues constituting the active site are identical with those of the chicken M1 type except for one amino acid substitution.

Amino Acid Sequence↗
PubMed1992

The amino acid sequence of nucleoside diphosphate kinase I from spinach leaves, as deduced from the cDNA sequence.

The primary structure of nucleoside diphosphate (NDP) kinase from spinach leaves has been deduced from its cDNA sequence. A lambda gt 11 cDNA library derived from spinach leaves was screened using an antibody against NDP kinase I, which we previously purified to electrophoretic homogeneity (T. Nomura, T. Fukui, and A. Ichikawa, 1991, Biochim. Biophys. Acta 1077, 47-55). The cDNA sequences of positive clones contained the amino acid coding region (444 base pairs) for NDP kinase I as well as 5' and 3' noncoding regions of 33 and 361 base pairs, respectively. The cDNAs hybridized to a 1.1-kb mRNA. NDP kinase I contains 148 amino acid residues with a molecular mass of 16,305, which is in excellent agreement with that of the purified enzyme (16 kDa). Homology was found between the sequence of spinach NDP kinase I and those of the rat, Myxococcus xanthus, and Dictyostelium discoideum NDP kinases, as well as the human Nm23-gene product and the awd protein of Drosophila melanogaster.

Amino Acid Sequence↗
PubMed2000

Improving quality of expressed sequence tag (EST) databases: recovery of reversed, antisense cDNA sequences.

Expressed sequence tag (EST) databases contain a significant number (5-20%) of reversed, antisense, cDNA sequences that can be recognized by the label "reversed clone: similarity on wrong strand" in the annotations to the sequence. Despite this high number of altered sequences, no attempt has been made to explain the alteration in molecular terms, or to evaluate their effect on the quality of the information curated in EST databases. In this paper we try to explain the way these altered sequences are originated, and propose a plausible mechanism: a "double priming" of the first strand oligo-dT primer at both ends of nascent cDNAs. In this way, a symmetrical cDNA intermediate is generated, an intermediate that can be cloned after partial digestion with the restriction enzyme used for the directional cloning. Furthermore, when "secondary" priming takes place inside the cDNA, the chain synthesized is prone to be truncated prematurely, with the subsequent loss of upstream information. One of the most subtle effects of this cloning alteration is the generation of virtual open reading frames (ORFs) in sequences with no homologues available for comparison. Nevertheless, and according to our model and our data, the "double priming mechanism" does not shift the ORF effected, so antisense sequences should be considered as normal ones after a simple transformation in their inverse-complementary forms.

Artifacts↗
PubMed1991

Rabbit hepatic lipase cDNA sequence: low activity is associated with low messenger RNA levels.

We have investigated a possible mechanism for the reported low activity of hepatic lipase (HL) in the rabbit by cloning and sequencing the cDNA for rabbit HL and using the clone to quantify mRNA levels. A 1.6 kb cDNA clone was sequenced and found to encode the mature protein of 477 amino acids and 20 amino acids of the hydrophobic leader peptide. A high degree of amino acid sequence identity was demonstrated with human (81%) and rat (79%) HL. The putative active site was well conserved, and mutations reported to reduce activity in HL or lipoprotein lipase were not present in the rabbit sequence. The activity and mRNA levels were compared with those of the rat, an animal possessing relatively high HL activity. In post-heparin plasma of the rat, HL activity was nine times greater than in that of the rabbit (24.9 +/- 1.6 units per ml plasma, n = 5 vs. 2.7 +/- 0.1, n = 5, P = 0.0001). Comparison of mRNA levels was made by dot blot analysis of liver poly (A+) RNA obtained from each species and probed with either rabbit or rat HL cDNA, labeled to the same specific radioactivity. Specific HL mRNA levels were found to be nine times greater in the rat than in the rabbit (8.90 +/- 0.11 units, n = 5 vs. 1.00 +/- 0.01, n = 5, P = 0.0001). Thus, low hepatic lipase activity in the rabbit is associated with low mRNA levels, suggesting that the observed species difference in activity is due to differences in the level of mRNA.

Amino Acid Sequence↗
PubMed1997

cDNA sequence and expression of bovine prodynorphin.

Prodynorphin (ProDYN) in the anterior pituitary gland appears to be processed differently from the brain, and the ProDYN-derived peptides may function differently in the anterior pituitary than in the brain. To further investigate the roles of ProDYN-derived peptides in the anterior pituitary, we have determined the nucleotide (nt) sequence of the cDNA encoding bovine ProDYN. This is the first time a complete cDNA sequence for ProDYN has been reported. The nt and deduced amino acid (aa) sequences were compared to the known ProDYN of other species. Northern blot analysis and reverse transcription-polymerase chain reaction (RT-PCR) combined with Southern blot analysis demonstrated that the expression of ProDYN in both the anterior and posterior pituitary glands was much lower than that in the neural tissues of the striatum and hypothalamus.

Amino Acid Sequence↗
PubMed2001

GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP.

The release of vast quantities of DNA sequence data by large-scale genome and expressed sequence tag (EST) projects underlines the necessity for the development of efficient and inexpensive ways to link sequence databases with temporal and spatial expression profiles. Here we demonstrate the power of linking cDNA sequence data (including EST sequences) with transcript profiles revealed by cDNA-AFLP, a highly reproducible differential display method based on restriction enzyme digests and selective amplification under high stringency conditions. We have developed a computer program (GenEST) that predicts the sizes of virtual transcript-derived fragments (TDFs) of in silico-digested cDNA sequences retrieved from databases. The vast majority of the resulting virtual TDFs could be traced back among the thousands of TDFs displayed on cDNA-AFLP gels. Sequencing of the corresponding bands excised from cDNA-AFLP gels revealed no inconsistencies. As a consequence, cDNA sequence databases can be screened very efficiently to identify genes with relevant expression profiles. The other way round, it is possible to switch from cDNA-AFLP gels to sequences in the databases. Using the restriction enzyme recognition sites, the primer extensions and the estimated TDF size as identifiers, the DNA sequence(s) corresponding to a TDF with an interesting expression pattern can be identified. In this paper we show examples in both directions by analyzing the plant parasitic nematode Globodera rostochiensis. Various novel pathogenicity factors were identified by combining ESTs from the infective stage juveniles with expression profiles of approximately 4000 genes in five developmental stages produced by cDNA-AFLP.

Animals↗
PubMed2002

cDNA sequence of porcine thioredoxin.

Several mammalian thioredoxin cDNA sequences, namely that of human, macaca, ovine, bovine, equine and murine have been already registered in the Genbank database; but that of porcine is still not known. In this communication, we report the full-length cDNA sequence of porcine thioredoxin as determined by RT-PCR method. We also compared the protein sequence of thioredoxin from various mammals. Multialignment of the amino acid sequences between porcine and other mammalian species revealed that the sequences are highly conserved. Only one difference exists between the amino acid sequences of porcine and bovine thioredoxin.

Amino Acid Sequence↗
PubMed1992

Evolution of vertebrate IgM: complete amino acid sequence of the constant region of Ambystoma mexicanum mu chain deduced from cDNA sequence.

cDNA clones coding for the constant region of the Mexican axolotl (Ambystoma mexicanum) mu heavy immunoglobulin chain were selected from total spleen RNA, using a cDNA polymerase chain reaction technique. The specific 5'-end primer was an oligonucleotide homologous to the JH segment of Xenopus laevis mu chain. One of the clones, JHA/3, corresponded to the complete constant region of the axolotl mu chain, consisting of a 1362-nucleotide sequence coding for a polypeptide of 454 amino acids followed in 3' direction by a 179-nucleotide untranslated region and a polyA+ tail. The axolotl C mu is divided into four typical domains (C mu 1-C mu 4) and can be aligned with the Xenopus C mu with an overall identity of 56% at the nucleotide level. Percent identities were particularly high between C mu 1 (59%) and C mu 4 (71%). The C-terminal 20-amino acid segment which constitutes the secretory part of the mu chain is strongly homologous to the equivalent sequences of chondrichthyans and of other tetrapods, including a conserved N-linked oligosaccharide, the penultimate cysteine and the C-terminal lysine. The four C mu domains of 13 vertebrate species ranging from chondrichthyans to mammals were aligned and compared at the amino acid level. The significant number of mu-specific residues which are conserved into each of the four C mu domains argues for a continuous line of evolution of the vertebrate mu chain. This notion was confirmed by the ability to reconstitute a consistent vertebrate evolution tree based on the phylogenic parsimony analysis of the C mu 4 sequences.

Ambystoma↗
PubMed2001

[Coding region cDNA sequence cloning of rat neuroglobin gene, its polymorphism feature and tissue expression profile analysis].

The coding region cDNA sequence of rat neuroglobin (NGB) was obtained by RT-PCR technique using a degeneracy PCR primer pair based on previously reported cDNA sequence of human and mouse NGB gene. Result demonstrated that the coding region cDNA sequence of rat NGB gene is 456 bp in length, which could encode a protein of 151 amino acids. The rat NGB gene is highly homology with mouse (96%) and human (88%) NGB gene. However, several polymorphism sites were also detected in the rat NGB coding region: 113 t/c [L38P], 133 a/g [N45D], 388 a/g[R130G], 417 t/c. The cDNA sequence of rat NGB gene has been registered in GenBank under the accession number AF333245. Moreover, highly expression level of rat NGB in brain, liver, kidney, heart and skeletal muscle was detected by using multiple tissue RT-PCR technique, indicating the functional importance of this novel gene.

Amino Acid Sequence↗
PubMed1985

Amino acid sequence of the alpha subunit of transducin deduced from the cDNA sequence.

Transducin, a GTP-binding protein involved in phototransduction in the vertebrate retina, belongs to a family of homologous coupling proteins that also includes Gs and Gi, the regulatory proteins of adenylate cyclase. Here we report the cDNA sequence and deduced amino acid sequence of transducin's alpha subunit (T alpha). The cDNA was isolated, by screening with an antibody probe, from a bovine retinal cDNA library in the expression vector lambda gt11. The 2.2-kilobase cDNA insert hybridized to a single 2.6-kilobase poly(A)+ RNA species present in extracts of bovine retina but not of bovine heart, liver, or brain. The nucleotide sequence of the cDNA revealed an open reading frame long enough to encode the entire 39-kDa T alpha polypeptide. The polypeptide sequence deduced from the cDNA would be composed of 350 amino acids and have a molecular weight of 39,971. Portions of the sequence matched reported amino acid sequences of T alpha tryptic fragments, including sites specifically ADP-ribosylated by cholera and pertussis toxins. The predicted sequence also includes four segments, ranging from 11 to 19 residues in length, that exhibit significant homology to sequences of GTP-binding proteins, including the ras proteins of man and yeast and the elongation factors of ribosomal protein synthesis in bacteria, EF-G and EF-Tu. In combination with previous functional studies of tryptic fragments of T alpha, the deduced amino acid sequence makes it possible to predict which portions of the polypeptide interact with other molecules involved in retinal phototransduction.

Amino Acid Sequence↗
PubMed2002

[Isolation and identification of cDNA sequence differentially expressed in human lung carcinoma].

BACKGROUND & OBJECTIVE: The molecular mechanism of the pathogenesis of lung carcinoma is unclear; because key genes related to lung carcinoma have not been identified. This study was designed to isolate and identify differentially expressed cDNA sequences in human lung carcinoma for cloning lung carcinoma-related genes. METHOD: Using mRNA differential display method combined with cloning and reserve Northern dot blot and sequencing and RT-PCR, differentially expressed cDNA sequences were isolated between two lung cancer cell lines, two adult lung carcinoma tissue and paired normal tissue of trachea epithelia. RESULT: Sixteen differentially expressed cDNA fragments were isolated, subsequent cloning of sixteen differentially expressed cDNA fragments were confirmed by reverse Northern dot blot and sequencing and BLAST analysis. Two of these were shown to be novel gene sequences that had not been reported. Eight of the remaining cDNA sequences homologize to known genes; additionally two differentially expressed cDNA sequences were confirmed by RT-PCR. CONCLUSION: Using mRNA differentially display, The authors had successfully isolated ten differentially expressed cDNA sequences from human lung carcinoma, these cDNA sequences might be involved in the pathogenesis of lung carcinoma.

Blotting, Northern↗
PubMed2007

cTrans: generating polypeptide databases from cDNA sequences.

cTrans is a comprehensive utility used to generate polypeptide databases from cDNA sequences. The goal is achieved through integrating four main functions, including retrieving sequences of species of interest from the downloaded packages from dbEST of GenBank, format conversion, checking and deleting vector and adaptor contamination, and translating the cDNA sequences in all six frames and selecting specific translations for database construction in a user-defined length threshold. In addition, this utility is also applicable to cDNA sequences produced by users themselves.

Base Sequence↗
PubMed1986

Chromosomal protein HMG-14. Complete human cDNA sequence and evidence for a multigene family.

The isolation and sequencing of cDNA clone coding for the entire sequence of human nonhistone chromosomal protein HMG-14 is described. Sequence analysis reveals that the open reading frame constitutes only 25% of the transcript, that the 5'-untranslated region is extremely rich in GC residues (75%), and that the 3'-untranslated region is highly enriched in AT residues. The amino acid sequence, deduced from the reading frame, is 94% homologous to the calf thymus protein suggesting evolutionary constraints on the conformation of the protein. The human genome contains 60-90 HMG-14 gene copy equivalents which, as suggested by Southern analysis, are not tandemly arranged. Northern analysis of RNA isolated from several sources reveals that a single-sized mRNA codes for this protein. Southern analysis reveals that cross-hybridizing sequences are present in the genome of several different species indicating that the evolutionary origin of this gene was over 350 million years ago. The overall features of the human HMG-14 cDNA are very similar to those of the human HMG-17 cDNA, and the number of gene equivalents present in the human genome is similar for the two proteins. However, their nucleotide sequence is significantly different indicating that the multigene family coding for HMG-14 is distinct from that coding for HMG-17.

Base Sequence↗
PubMed1993

Adipose pyruvate carboxylase: amino acid sequence and domain structure deduced from cDNA sequencing.

The complete amino acid sequence of 3T3-L1 adipocyte pyruvate carboxylase (PC) [pyruvate:carbon-dioxide ligase (ADP-forming), EC 6.4.1.1] has been deduced from sequencing overlapping cDNA clones obtained from an adipocyte cDNA library constructed in the lambda Zap vector. The encoding mRNA for PC promoter contains 4067 nt, including a 3534-nt coding sequence and noncoding regions of 100 and 433 nt at the 5' and 3' ends, respectively. The biotinylated lysine of the encoded PC promoter (1178 amino acids with a calculated M(r) of apocarboxylase = 129,784) is located 35 residues from the COOH-terminal end and, as in most other biotin enzymes, is in the consensus sequence AMKM. The adipocyte PC is closely similar (53% identity) to the yeast enzyme and contains different segments that are homologous with regions from the biotin carboxylase component of Escherichia coli acetyl-CoA carboxylase, the keto acid-binding subunits of Propionibacterium shermanii oxaloacetate transcarboxylase and Klebsiella pneumoniae oxaloacetate decarboxylase, and to the biotin carboxyl-carrier protein of the bacterial biotin enzymes. In addition to the putative mitochondrial targeting signal, functional domains are readily identifiable in the sequence and are in the following order: biotin carboxylase-carboxyltransferase-biotin carboxyl-carrier protein, as proposed for yeast PC.

3T3 Cells↗
PubMed2003

cDNA sequence analysis of seven peptide toxins from the spider Selenocosmia huwena.

Seven cDNAs encoding six toxins HWTX-I, HWTX-II, HWTX-IIIa, HWTX-IV, HWTX-V, HWTX-VII and one lectin SHL-I, from the spider Selenocosmia huwena, were cloned and sequenced. On the basis of their amino acid sequences, we designed and synthesized 3' RACE and 5' RACE primer. By overlapping the two partial cDNA sequences obtained by 3' and 5' RACE, their full-length cDNA sequences were obtained. All of the cDNAs of these seven peptides encode a precursor including a potential signal peptide of 21-24 residues, a mature toxin of about 30 residues and an intervening pro region. The prepro regions of HWTX-I, HWTX-IIIa, HWTX-IV, HWTX-V and SHL-I were demonstrated, by the comparison of the cDNA sequences, to have high similarity, which is concert with the similar inhibitor cystine knot motif of HWTX-I, HWTX-IV and SHL-I although their functions are different. It was also demonstrated that, HWTX-II and HWTX-VII share the highly similar prepro region which is different from that of HWTX-I, HWTX-IV and SHL-I. The three dimensional structure of HWTX-II has been determined to exhibit a different motif. This indicates that the seven peptides from S. huwena could be classified into two different superfamilies according to the prepro region of cDNA sequences.

Amino Acid Sequence↗