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PubMed2001

Establishment of a high throughput EST sequencing system using poly(A) tail-removed cDNA libraries and determination of 36,000 bovine ESTs.

We determined 36,310 bovine expressed sequence tag (EST) sequences using 10 different cDNA libraries. For massive EST sequencing, we devised a new system with two major features. First, we constructed cDNA libraries in which the poly(A) tails were removed using nested deletion at the 3'-ends. This permitted high quality reading of sequences from the 3'-end of the cDNA, which is otherwise difficult to do. Second, we increased throughput by sequencing directly on templates generated by colony PCR. Using this system, we determined 600 cDNA sequences per day. The read-out length was >450 bases in >90% of the sequences. Furthermore, we established a data management system for analyses, storage and manipulation of the sequence data. Finally, 16,358 non-redundant ESTs were derived from approximately 6900 independent genes. These data will facilitate construction of a precise comparative map across mammalian species and isolate the functional genes that govern economic traits. This system is applicable to other organisms, including livestock, for which EST data are limited.

Animals↗
PubMed1999

Analysis of expressed sequence tags of porcine skeletal muscle.

Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Therefore, to progress towards a better understanding of the genetic factors influencing these traits, the first step is to characterize the genes expressed in skeletal muscle tissue in pig. To this aim, we constructed a porcine biceps femoris muscle cDNA library and sequenced 111 randomly isolated clones. By FASTA analysis, we identified 72 unique clones: 47 showed homology to previously identified genes in human or other mammals, 20 matched uncharacterized expressed sequence tags (ESTs), two showed no significant matches to sequences already present in DNA databases, and three other clones containing only repetitive elements were excluded from further analysis. Mitochondrial genes (16.2%), myosin heavy chain genes (9%) and the actin alpha skeletal muscle gene (9%) were the most abundant transcripts. Among the 47 identified genes several muscle-specific or predominant sequences expressed in skeletal muscle were found. The sequences of the clones matching uncharacterized human, mouse or porcine ESTs were tested by GRAIL in order to identify putative coding regions. The results of our analysis allowed the establishment of a first list of genes expressed in porcine skeletal muscle.

Amino Acid Sequence↗
PubMed2002

Molecular cloning and characterization of a novel mouse macrophage C-type lectin, mMGL2, which has a distinct carbohydrate specificity from mMGL1.

A novel mouse macrophage galactose-type C-type lectin 2 (mMGL2) was identified by BLAST analysis of expressed sequence tags. The sequence of mMGL2 is highly homologous to the mMGL, which should now be called mMGL1. The open reading frame of mMGL2 contains a sequence corresponding to a type II transmembrane protein with 332 amino acids having a single extracellular C-type lectin domain. The 3'-untranslated region included long terminal repeats of mouse early transposon. The Mgl2 gene was cloned from a 129/SvJ mouse genomic library and sequenced. The gene spans 7,136 base pairs and consists of 10 exons, which is similar to the genomic organization of mMGL1. The reverse transcriptase-PCR analysis indicates that mMGL2 is expressed in cell lines and normal mouse tissues in a macrophage-restricted manner, also very similar to that of mMGL1. The mMGL2 mRNA was also detected in mMGL1-positive cells, which were sorted from thioglycollate-induced peritoneal cells with a mMGL1-specific monoclonal antibody, LOM-8.7. The soluble recombinant proteins of mMGL2 exhibited carbohydrate specificity for alpha- and beta-GalNAc-conjugated soluble polyacrylamides, whereas mMGL1 preferentially bound Lewis X-conjugated soluble polyacrylamides in solid phase assays. These two lectins may function cooperatively as recognition and endocytic molecules on macrophages and related cells.

3' Untranslated Regions↗
PubMedDate not supplied

Gene expression profiling in islet biology and diabetes research.

Following the sequencing of most of the human and mouse genomes, the next task for physicians and scientists will be to assess the relative levels of expression of these genes during development, following exposure to various nutritional and pharmacological conditions, and in disease states such as diabetes and related metabolic disorders. This review provides an overview of the various methodologies available for monitoring global gene expression. Use of cDNA libraries, Expressed Sequence Tag (EST) sequencing projects and databases, differential display (DD), serial analysis of gene expression (SAGE), subtractive cloning, and both cDNA and oligo microarrays are discussed, along with their merits and limitations. The Endocrine Pancreas Consortium http://www.cbil.upenn.edu/EPConDB/ has constructed mouse and human cDNA libraries from adult and various stages of embryonic development of endocrine pancreas. Over 100,000 ESTs have been deposited in public databases, and each clone is available through the IMAGE Consortium. A guide to Internet access is provided for future investigation.

Animals↗
PubMed1986

Structure of mouse type IV collagen. Amino-acid sequence of the C-terminal 511-residue-long triple-helical segment of the alpha 2(IV) chain and its comparison with the alpha 1(IV) chain.

The sequence of 511 residues from the C-terminal portion of the triple helix of mouse alpha 2(IV) chain was determined by using the pepsin fragment P2 of collagen IV and two cDNA clones selected from an Engelbreth-Holm-Swarm (EHS) tumor library. The sequence contains nine interruptions of the triplet repeat Gly-Xaa-Yaa ranging in size from single insertions or deletions up to stretches of eleven amino acid residues. Five of these interruptions match those present in the homologous segment of the alpha 1(IV) chain but are otherwise different in length and/or sequence. A low homology was found for the triplet regions of the alpha 1(IV) and alpha 2(IV) chain which constitute more than 90% of the sequence. The data indicate a remote evolutionary relationship of the triple-helical sequences of the two constituent chains of basement membrane collagen.

Amino Acid Sequence↗
PubMed1993

Isolation, characterization, and expression of a cDNA encoding N-acetylglucosaminyltransferase V.

A cDNA clone for the complete coding sequence for alpha-1,3(6)-mannosylglycoprotein beta-1,6-N-acetylglucosaminyltransferase V (GlcNAc-T V, EC 2.4.1.155) was isolated and expressed in COS-7 cells. Degenerate oligonucleotide primers for polymerase chain reaction were synthesized based on the amino acid sequence of three tryptic peptides isolated from affinity-purified GlcNAc-T V. Polymerase chain reaction amplimers were isolated from rat and mouse mRNA. A cDNA-encoding full-length enzyme was isolated from a rat 1 cell (EJ-ras-transformed) library and sequenced. Transient expression of this clone in COS-7 cells, followed by enzymatic activity assays, demonstrated that this cDNA sequence encodes GlcNAc-T V. Northern analysis of rat kidney mRNA revealed a single band corresponding to a length of about 7 kilobases. Sequence analysis of the cDNA clone demonstrated an open reading frame that encoded a type II membrane protein of 740 amino acids.

Amino Acid Sequence↗
PubMed1997

Identification of three allatostatins and their cDNA from the mosquito Aedes aegypti.

Three allatostatins have been isolated from the mosquito Aedes aegypti. These peptides have the following structures: Ser-Pro-Lys-Tyr-Asn-Phc-Gly-Leu-amide, Leu-Pro-His-Tyr-Asn-Phe-Gly-Leu-amide, and Arg-Val-Tyr-Asp-Phe-Gly-Leu-amide. A cDNA encoding these peptides was isolated from an abdominal ganglia cDNA library and sequenced. It was found to encode two additional allatostatins: Ala-Ser-Ala-Tyr-Arg-Tyr-His-Phe-Gly-Leu-amide and Leu-Pro-Asn-Arg-Tyr-Asn-Phe-Gly-Leu-amide. Northern analysis of whole mosquito mRNA revealed a single prepro-allatostatin message of around 3,000 bases. Identification of a partial prepro-allatostatin cDNA from a midgut cDNA library shows that the same gene is also expressed in the mosquito midgut.

Aedes↗
PubMed1985

Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations.

Synthetic probes deduced from amino acid sequence data are widely used to detect cognate coding sequences in libraries of cloned DNA segments. The redundancy of the genetic code dictates that a choice must be made between (1) a mixture of probes reflecting all codon combinations, and (2) a single longer "optimal" probe. The second strategy is examined in detail. The frequency of sequences matching a given probe by chance alone can be determined and also the frequency of sequences closely resembling the probe and contributing to the hybridization background. Gene banks cannot be treated as random associations of the four nucleotides, and probe sequences deduced from amino acid sequence data occur more often than predicted by chance alone. Probe lengths must be increased to confer the necessary specificity. Examination of hybrids formed between unique homologous probes and their cognate targets reveals that short stretches of perfect homology occurring by chance make a significant contribution to the hybridization background. Statistical methods for improving homology are examined, taking human coding sequences as an example, and considerations of codon utilization and dinucleotide frequencies yield an overall homology of greater than 82%. Recommendations for probe design and hybridization are presented, and the choice between using multiple probes reflecting all codon possibilities and a unique optimal probe is discussed.

Amino Acid Sequence↗
PubMed1997

Differential expression of transforming growth factor-beta receptors in rat kidney development.

Transforming growth factor-beta 1 (TGF-beta 1) is strongly expressed during embryogenesis and in sites undergoing intense development and morphogenesis. Two receptor serine/threonine kinases (types I and II) have been identified as signal-transducing TGF-beta receptors. This study was undertaken to further explore the role of the distinct TGF-beta receptors during kidney development. The species-specific sequence information for the two T beta R-I, namely, activin receptor-like kinase-5 (ALK-5) and Tsk7L, in the rat was sought. Two full-length T beta R-I cDNAs were cloned from a neonatal rat kidney and lung libraries, and sequencing revealed that they were the rat homologs of human ALK-5 and murine Tsk7L. Both types I and II TGF-beta receptors are expressed in the kidney as determined by Northern blot analysis. T beta R-II mRNA abundance was significantly greater in the neonatal rat kidney compared with the adult rat kidney. Similarly, ALK-5 mRNA was more highly expressed in the fetal and neonatal rat kidney than the adult rat kidney. In contrast, there was no significant difference in Tsk7L mRNA abundance among the fetal, neonatal, and adult rat kidney. Thus, based on these findings, both T beta R-II and ALK-5 are developmentally regulated in the kidney. Increased expression of T beta R-II and ALK-5 proteins in the developing kidney was confirmed by immunohistochemistry. Interestingly, the two TGF-beta receptors did not entirely colocalize, raising the intriguing possibility that other TGF-beta signaling receptors may be involved.

Activin Receptors, Type I↗
PubMed1997

Sequence and developmental expression of Cyp18, a member of a new cytochrome P450 family from Drosophila.

Preliminary studies of a partial cDNA clone of the Eig17-1 gene from Drosophila melanogaster have shown that it encodes a probable cytochrome P450 of unknown function. To further characterize the Eig17-1 gene product, a full-length cDNA clone was isolated from a late-larval cDNA library and sequenced. Eig17-1 encodes a protein of 538 amino acids. The predicted protein is a cytochrome P450 that has been assigned to a new family, CYP18. The CYP18 protein is most closely related to steroid and xenobiotic metabolizing P450s of family CYP2 (30-33% identity), and to vertebrate steroidogenic P450s of families CYP17 and CYP21 (25-28% identity). Developmental Northern blot analysis revealed five distinct periods of Cyp18 expression during postembryonic development. Each period lasted 12-15 h, and was tightly correlated with reported ecdysteroid pulses in the first, second and third larval instars, at the time of pupariation and in pupae. This pattern of expression is consistent with the known induction of Cyp18 transcription by 20-hydroxyecdysone at the time of pupariation and suggests that ecdysteroids are major regulators of Cyp18 expression throughout postembryonic development. Northern blot analysis of RNA isolated from different prepupal tissues indicates that Cyp18 is differentially expressed in various ecdysteroid-responsive tissues. High Cyp18 expression was observed in body wall and gut while negligible expression was observed in salivary glands and fat body.

Amino Acid Sequence↗
PubMed1994

Plasma alpha-1-antiproteinase from the Mongolian gerbil, Meriones unguiculatus: isolation, partial characterization, sequencing of cDNA, and implications for molecular evolution.

alpha-1-Antiproteinase (also called alpha-1-proteinase inhibitor or alpha-1-antitrypsin) with a molecular mass of 56 kDa was purified from plasma of the Mongolian gerbil, Meriones unguiculatus, to apparent homogeneity. It inhibited trypsin, chymotrypsin, elastase, and plasmin, but not kallikrein or thrombin. Eight cDNA clones coding for this protein were isolated from a liver cDNA library and sequenced. They contained the same coding regions consisting of a 24-residue signal peptide and a 382-residue mature protein. The reactive site sequence (P3-P3) was Val-Pro-Met-Ser-Ile-Pro, characteristic of alpha-1-antiproteinase of orthodox type [Suzuki, Y. et al. (1991) J. Biol. Chem. 266, 928-932]. A molecular phylogenetic tree of 11 orthologous inhibitors, constructed on the basis of the synonymous substitution rate, shows (i) that the reactive site region is highly conserved as compared to the other part of the molecule, which contrasts with the generally accepted view that the reactive site region of serpins is strongly hypervariable, and (ii) that the myomorphs (gerbil, rat, and two species of mouse, i.e. Mus domesticus and Mus caroli) and the caviomorph (guinea pig) fail to consist of a monophyletic order, which also contradicts the traditional taxonomy based on the morphology. In the present tree, the guinea pig joins the lagomorph (rabbit), and is rather widely separated from the myomorph branch. The result, however, supports the recent hypothesis based on the molecular evolution of several other proteins that the guinea pig does not belong to the same order as the myomorph, and the caviomorphs should be elevated in taxonomic rank and conferred an ordinal status distinct from the rodents.

Amino Acid Sequence↗
PubMed1995

Novel avidin and streptavidin binding sequences found in synthetic peptide libraries.

Synthetic resin-bound peptide libraries made of protein L-amino acids have been synthesized. During screening of the libraries, peptides that bind to avidin have been identified containing a novel motif with two histidines separated by one residue. A sub-library was synthesized and screened, and new critical residues appeared surrounding the two histidines. Additionally peptide libraries made of D-amino acids have been screened with avidin and streptavidin and novel motifs have been found.

Amino Acid Sequence↗
PubMed1988

Cloning and nucleotide sequence of placental hGH-V cDNA.

We have previously demonstrated the presence in human placenta and maternal serum of a GH variant, called human placental growth hormone (hPGH). We have also shown that the hGH-V gene is expressed at the placental level thus possibly coding for hPGH. The hGH-V cDNA has now been isolated from a lambda gt 11 human placenta cDNA library. Its sequence has been determined which firmly establishes the GH-V gene mode of splicing as well as the GH-V protein structure. Our data give final evidence of placental hGH-V gene expression and reinforce the hypothesis of identity between the hGH-V protein and hPGH.

Amino Acid Sequence↗
PubMed1987

Alternative splicing of human elastin mRNA indicated by sequence analysis of cloned genomic and complementary DNA.

Poly(A)+ RNA, isolated from a single 7-mo fetal human aorta, was used to synthesize cDNA by the RNase H method, and the cDNA was inserted into lambda gt10. Recombinant phage containing elastin sequences were identified by hybridization with cloned, exon-containing fragments of the human elastin gene. Three clones containing inserts of 3.3, 2.7, and 2.3 kilobases were selected for further analysis. Three overlapping clones containing 17.8 kilobases of the human elastin gene were also isolated from genomic libraries. Complete sequence analysis of the six clones demonstrated that: the cDNA encompassed the entire translated portion of the mRNA encoding 786 amino acids, including several unusual hydrophilic amino acid sequences not previously identified in porcine tropoelastin, exons encoding either hydrophobic or crosslinking domains in the protein alternated in the gene, and a great abundance of Alu repetitive sequences occurred throughout the introns. The data also indicated substantial alternative splicing of the mRNA. These results suggest the potential for significant variation in the precise molecular structure of the elastic fiber in the human population.

Amino Acid Sequence↗
PubMed2004

Expansins abundant in secondary xylem belong to subgroup A of the alpha-expansin gene family.

Differentiation of xylem cells in dicotyledonous plants involves expansion of the radial primary cell walls and intrusive tip growth of cambial derivative cells prior to the deposition of a thick secondary wall essential for xylem function. Expansins are cell wall-residing proteins that have an ability to plasticize the cellulose-hemicellulose network of primary walls. We found expansin activity in proteins extracted from the cambial region of mature stems in a model tree species hybrid aspen (Populus tremula x Populus tremuloides Michx). We identified three alpha-expansin genes (PttEXP1, PttEXP2, and PttEXP8) and one beta-expansin gene (PttEXPB1) in a cambial region expressed sequence tag library, among which PttEXP1 was most abundantly represented. Northern-blot analyses in aspen vegetative organs and tissues showed that PttEXP1 was specifically expressed in mature stems exhibiting secondary growth, where it was present in the cambium and in the radial expansion zone. By contrast, PttEXP2 was mostly expressed in developing leaves. In situ reverse transcription-PCR provided evidence for accumulation of mRNA of PttEXP1 along with ribosomal rRNA at the tips of intrusively growing xylem fibers, suggesting that PttEXP1 protein has a role in intrusive tip growth. An examination of tension wood and leaf cDNA libraries identified another expansin, PttEXP5, very similar to PttEXP1, as the major expansin in developing tension wood, while PttEXP3 was the major expansin expressed in developing leaves. Comparative analysis of expansins expressed in woody stems in aspen, Arabidopsis, and pine showed that the most abundantly expressed expansins share sequence similarities, belonging to the subfamily A of alpha-expansins and having two conserved motifs at the beginning and end of the mature protein, RIPVG and KNFRV, respectively. This conservation suggests that these genes may share a specialized, not yet identified function.

Amino Acid Sequence↗
PubMed2005

Monoterpene metabolism. Cloning, expression, and characterization of menthone reductases from peppermint.

(-)-Menthone is the predominant monoterpene produced in the essential oil of maturing peppermint (Mentha x piperita) leaves during the filling of epidermal oil glands. This early biosynthetic process is followed by a second, later oil maturation program (approximately coincident with flower initiation) in which the C3-carbonyl of menthone is reduced to yield (-)-(3R)-menthol and (+)-(3S)-neomenthol by two distinct NADPH-dependent ketoreductases. An activity-based in situ screen, by expression in Escherichia coli of 23 putative redox enzymes from an immature peppermint oil gland expressed sequence tag library, was used to isolate a cDNA encoding the latter menthone:(+)-(3S)-neomenthol reductase. Reverse transcription-PCR amplification and RACE were used to acquire the former menthone:(-)-(3R)-menthol reductase directly from mRNA isolated from the oil gland secretory cells of mature leaves. The deduced amino acid sequences of these two reductases share 73% identity, provide no apparent subcellular targeting information, and predict inclusion in the short-chain dehydrogenase/reductase family of enzymes. The menthone:(+)-(3S)-neomenthol reductase cDNA encodes a 35,722-D protein, and the recombinant enzyme yields 94% (+)-(3S)-neomenthol and 6% (-)-(3R)-menthol from (-)-menthone as substrate, and 86% (+)-(3S)-isomenthol and 14% (+)-(3R)-neoisomenthol from (+)-isomenthone as substrate, has a pH optimum of 9.3, and K(m) values of 674 mum, > 1 mm, and 10 mum for menthone, isomenthone, and NADPH, respectively, with a k(cat) of 0.06 s(-1). The recombinant menthone:(-)-(3R)-menthol reductase has a deduced size of 34,070 D and converts (-)-menthone to 95% (-)-(3R)-menthol and 5% (+)-(3S)-neomenthol, and (+)-isomenthone to 87% (+)-(3R)-neoisomenthol and 13% (+)-(3S)-isomenthol, displays optimum activity at neutral pH, and has K(m) values of 3.0 mum, 41 mum, and 0.12 mum for menthone, isomenthone, and NADPH, respectively, with a k(cat) of 0.6 s(-1). The respective activities of these menthone reductases account for all of the menthol isomers found in the essential oil of peppermint. Biotechnological exploitation of these genes could lead to improved production yields of (-)-menthol, the principal and characteristic flavor component of peppermint.

Amino Acid Motifs↗
PubMed1987

Identification of atrial natriuretic factor gene transcripts in the central nervous system of the rat.

Atrial natriuretic factor (ANF) gene transcripts have been identified in the hypothalamus, brainstem, and cerebral cortex of the rat. The hypothalamic transcripts are similar in overall size (approximately 1100 nucleotides), 5' terminus, 3' terminus, and nucleotide sequence to their counterparts synthesized in the cardiac atria. The 5' terminus of the hypothalamic transcripts, determined by both S1 nuclease and primer-extension analysis, was located approximately 20 nucleotides downstream from the TATAAAA sequence that is thought to dictate the start of transcription. Similar 5' termini were identified in RNA from the brainstem and cerebral cortex. The 3' termini of the hypothalamic transcripts mapped approximately 10 nucleotides downstream from each of two successive AATAAA sequences that are believed to provide the cleavage signal required for subsequent polyadenylylation. The same 3' termini were present in atrial, ventricular, lung, and pituitary RNA. To confirm the identity of the hypothalamic gene transcript, a partial-length cDNA clone encoding ANF was isolated from a hypothalamic cDNA library and sequenced. This hypothalamic clone was identical to an analogous atrial cDNA clone at each of its 612 nucleotide positions. These findings suggest that ANF peptides, previously identified in specific loci of the hypothalamus and pontine tegmentum, are synthesized locally in these tissues and support a role for this peptide in the central regulation of cardiovascular physiology.

Amino Acid Sequence↗