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Midgut proteases from Mamestra configurata (Lepidoptera: Noctuidae) larvae: characterization, cDNA cloning, and expressed sequence tag analysis.

The activities of digestive protease within the midgut of Mamestra configurata (bertha armyworm) larvae were examined using specific substrates and protease inhibitors. The bulk of the activity was associated with serine proteases comprising trypsin-, chymotrypsin-, and elastase-like enzymes. At least 10-15 serine protease isozymes were detected using one-dimension gelatin gel electrophoresis. Cysteine or aspartic protease activities were not present; however, amino- and carboxypeptidase activities were associated with the midgut extract. Midgut proteases were active in the pH range of 5.0-12.0 with peaks at pH 7.5 and 11.0. In general, the middle region of the midgut exhibited a higher pH (approximately 8.0) than either the posterior or anterior regions (approximately 7.3-7.7). Moulting larvae possessed a neutral gut pH that was 0.5-1.5 units below that of feeding larvae. Degenerate PCR and expressed sequence tag (EST)-based approaches were used to isolate 30 distinct serine protease encoding cDNAs from a midgut-specific cDNA library including 8 putative trypsins, 9 chymotrypsins, 1 elastase, and 12 whose potential activities could not be determined. cDNAs encoding three amino- and two carboxypeptidases were also identified. Larvae feeding upon artificial diet containing 0.2% soybean trypsin inhibitor experienced a significant delay in development.

Amino Acid Sequence↗

Molecular cloning and functional expression of human deoxyhypusine synthase cDNA based on expressed sequence tag information.

Deoxyhypusine synthase is an NAD(+)-dependent enzyme that catalyses the formation of a deoxyhypusine residue on the eukaryotic initiation factor 5A (eIF-5A) precursor by transferring an aminobutyl moiety from spermidine to the epsilon-amino group of a unique lysine residue. We have recently cloned and characterized the Neurospora crassa deoxyhypusine synthase cDNA using a reverse genetics approach. A GenBank search showed that a stretch of the deduced amino acid sequence (96 amino acids) of Neurospora deoxyhypusine synthase matches a short human expressed sequence tag (EST), Z25337, with greater than 70% amino acid identity. Gene-specific primers based on this EST were used together with universal primers to obtain 1219 bp and 1078 bp cDNAs from a human cDNA library. The 1219 bp and 1078 bp sequences, each containing an open reading frame, encode polypeptides of respectively 368 and 321 amino acids. The short sequence is identical to the long one except that it is missing a stretch of 47 amino acids spanning residues 261-307. The 368-amino-acid sequence of human deoxyhypusine synthase shares a high degree of identity ( > 50%) and similarity ( > 60%) with that of the Neurospora and yeast deoxyhypusine synthases. After cloning into an expression vector, the 368-amino-acid recombinant protein exhibits high deoxyhypusine synthase activity. In contrast, the 321-amino-acid recombinant protein shows no detectable activity.

Amino Acid Sequence↗

Sequence analysis of a 33.2 kb segment from the left arm of yeast chromosome XV reveals eight known genes and ten new open reading frames including homologues of ABC transporters, inositol phosphatases and human expressed sequence tags.

The complete nucleotide sequence of a 33221 bp segment, contained in cosmid pEOA1044, derived from the left arm of chromosome XV of Saccharomyces cerevisiae, appears in public databases between coordinates 177013 and 210234 (http://speedy.mips.biochem.mpg.de/). Computer analysis of that sequence revealed the presence of the previously known genes IRA2, DEC1, NUF2, HST1, RTG1, RIB2 and HAL2, one previously partially sequenced open reading frame (ORF) of unknown function (SCORFAC) and ten newly identified ORFs. One of the new ORFs is similar to the Drosophila melanogaster white gene and other transmembrane ABC transporters, another one has similarities to inositol phosphatases and others are similar to ORFs of unknown function from various organisms, including human Expressed Sequence Tags (ESTs). Potential transmembrane regions, ATP/GTP-binding and WD motifs have also been identified. The existence of yeast ESTs for two of the newly identified ORFs indicates that they are transcribed.

ATP-Binding Cassette Transporters↗

Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags.

Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for inferring gene structures from predicted exon candidates, based on Expressed Sequence Tags (ESTs) and biological intuition/rules. The algorithm first finds all the related ESTs in the EST database (dbEST) for each predicted exon, and infers the boundaries of one or a series of genes based on the available EST information and biological rules. Then it constructs gene models within each pair of gene boundaries, that are most consistent with the EST information. By exploiting EST information and biological rules, the algorithm can (1) model complicated multiple gene structures, including embedded genes, (2) identify falsely-predicted exons and locate missed exons, and (3) make more accurate exon boundary predictions. The algorithm has been implemented and tested on long genomic sequences with a number of genes. Test results show that very accurate (predicted) gene models can be expected when related ESTs exist for the predicted exons.

Algorithms↗

The proteome of maize leaves: use of gene sequences and expressed sequence tag data for identification of proteins with peptide mass fingerprints.

As a first step in establishing a proteome database for maize, we have embarked on the identification of the leaf proteins resolved on two-dimensional (2-D) gels. We detected nearly 900 spots on the gels with a pH 4-7 gradient and over 200 spots on the gels with a pH 6-11 gradient when the proteins were visualized with colloidal Coomassie blue. Peptide mass fingerprints for 300 protein spots were obtained with matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer and 149 protein spots were identified using the protein databases. We also searched the pdbEST databases to identify the leaf proteins and verified 66% of the protein spots that had been identified using the protein databases. Sixty-seven additional protein spots were identified from expressed sequence tags (ESTs). Many abundant leaf proteins are present in multiple spots. Functions of over 50% of the abundant leaf proteins are either unknown or hypothetical. Our results show that EST databases in conjunction with peptide mass fingerprints can be used for identifying proteins from organisms with incomplete genome sequence information.

Electrophoresis, Gel, Two-Dimensional↗

Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags.

Intrahepatic cholangiocarcinoma (ICC), a malignant tumor derived from the bile duct epithelium, is one of the leading causes of death from cancer, worldwide. However, the mechanisms related to it remain largely unknown. In this study, an analysis of the gene expression profiles for ICC was done using the frequency of the ESTs obtained from nine cDNA libraries that constructed from 4 ICC cell lines and 4 normal liver tissues. One hundred and thirty-seven genes were identified as being either up- or down-regulated in human ICC cells. Thirty genes were randomly selected to confirm their differential expression in 4 human ICC cell lines and 5 ICC tissues compared to normal liver tissues by semi-quantitative RT-PCR. Among these genes, ANXA1, ANXA2, AMBP, and SERPINC1 were further verified by immunohistochemical analyses. In conclusion, these identified genes represent potential biomarkers for ICC and represent potential targets for elucidating the molecular mechanisms that are associated with ICC.

Bile Duct Neoplasms↗

Isolation of 115 human chromosome 8-specific expressed-sequence tags by exon amplification.

Exon-amplification experiments were undertaken to isolate potentially transcribable sequences from cosmid clones that previously had been mapped to subchromosomal bands of human chromosome 8 by fluorescence in situ hybridization. From 253 cosmids subjected to this procedure so far, we isolated 169 fragments and confirmed that they had been derived from the original cosmid clones. Among them, 38 revealed homology to repetitive DNA sequences such as Alu and L1 elements. The other 131 were unique sequences, but of these only 115 contained discernible open reading frames. Among these 115 sequences, 15 were identical to parts of six known genes listed in the public database. On the basis of information derived from mapping the original cosmid clones, we were able to localize two of these known genes, zinc finger protein 7 and heat shock transcription factor 1, to 8q24.3. Furthermore, we have proven that some of these clones are parts of the transcribed products by an exon connection method or by isolation of a novel cDNA that is homologous to murine clathrin-associated protein. The expressed-sequence tags isolated here will be useful resources for a transcriptional map of chromosome 8 and for isolation of new genes.

Adaptor Proteins, Vesicular Transport↗

Isolation of Cryptococcus neoformans chromosome-specific probes using expressed sequence tags.

Clinical and environmental isolates of Cryptococcus neoformans exhibit a high degree of karyotypic variability. Analysis of the molecular basis of karyotypic differences requires a large set of chromosome-specific probes. We have determined the chromosomal distribution of a set of randomly selected C. neoformans cDNA clones and have explored the feasibility of identifying these clones through partial DNA sequencing. Forty-four randomly selected cDNA clones were labelled and hybridized to PFGE blots of C. neoformans. Expressed sequence tags were generated by sequencing the 5'-end of each clone. Thirty-five clones hybridized to single bands on PFGE blots. At least seven chromosomes were recognized by these probes. Homology searches identified potential homologs of several groups of proteins not previously studied in C. neoformans. PFGE hybridization and sequencing of random cDNA clones is an efficient method for identifying chromosomal-specific probes in fungi that lack extensive sets of genetic markers.

Chromosomes, Fungal↗

Expressed sequence tags of medaka (Oryzias latipes) liver mRNA.

A medaka liver cDNA library was constructed in lambda ZAPII. The number of clones in this library is approximately 5 x 10(6). Three hundred sixty-one clones were randomly selected and, of these, 33 clones with over 1 kb were sequenced. These sequences were compared with GenBank and the dbEST (Re.96.0). Twenty-five clones of these 33 clones encoded 18 different genes and 2 different expressed sequence tags (ESTs). Sequences of 10 of the 18 clones had not previously been reported in fish. The codon usage of medaka genes is similar to that of Xenopus, mouse, and human genes, but not similar to that of yeast and Escherichia coli genes.

Animals↗

Digital cloning: identification of human cDNAs homologous to novel kinases through expressed sequence tag database searching.

Identification of novel kinases based on their sequence conservation within kinase catalytic domain has relied so far on two major approaches, low-stringency hybridization of cDNA libraries, and PCR method using degenerate primers. Both of these approaches at times are technically difficult and time-consuming. We have developed a procedure that can significantly reduce the time and effort involved in searching for novel kinases and increase the sensitivity of the analysis. This procedure exploits the computer analysis of a vast resource of human cDNA sequences represented in the expressed sequence tag (EST) database. Seventeen novel human cDNA clones showing significant homology to serine/threonine kinases, including STE-20, CDK- and YAK-related family kinases, were identified by searching EST database. Further sequence analysis of these novel kinases obtained either directly from EST clones or from PCR-RACE products confirmed their identity as protein kinases. Given the rapid accumulation of the EST database and the advent of powerful computer analysis software, this approach provides a fast, sensitive, and economical way to identify novel kinases as well as other genes from EST database.

Amino Acid Sequence↗

Large-scale generation and analysis of expressed sequence tags from porcine ovary.

One method to identify the factors that control ovarian function is to characterize the genes that are expressed in ovary. In the present study, cDNA libraries from fetal, neonatal, and prepubertal porcine ovaries, pubertal ovaries on different days of the estrous cycle (Days 0 [follicle], 5, and 12 [follicle and corpus luteum]), and follicles isolated from weaned sows (diameter, 2, 4, 6, and 8 mm) were constructed and sequenced. A total of 22 176 cDNAs were sequenced, of which 15 613 were of sufficient quality for clustering. Clustering of cDNAs resulted in 8507 contigs, 6294 (74%) of which were comprised of a single sequence. Sixty-eight percent of the contigs had consensus sequences that were homologous to existing Tentative Consensus (TC) sequences or mature transcripts (ET) in The Institute for Genomic Research Porcine Gene Index. The consensus sequences were classified according to the Gene Ontology Index. Most cDNA-encoded proteins were components of the nucleus, ribosome, or mitochondrion. The proteins primarily functioned in binding, catalysis, and transport. Nearly 75% of the proteins were involved in metabolism and cell growth and/or maintenance. Analysis of the cDNA frequency across different libraries demonstrated differential gene expression within different-size follicles, between follicles and corpora lutea, and across developmental time-points. The expression of selected genes (analyzed by ribonuclease protection assay and Northern blotting) was consistent with the frequency of their respective cDNA in the individual libraries. This porcine ovary unigene set will be useful for identifying factors and mechanisms controlling ovarian follicular development in a variety of species.

Animals↗

Acquisition of expressed sequence tags from Schistosoma japonicum cercariae (mainland China strain) and its homology analysis.

OBJECTIVE: To understand the general profiles of the genes included in Schistosoma japonicum (Sj) cercarriae cDNA library that we have constructed for the purpose of identifying novel genes. METHODS: The phages in Sj cercariae cDNA library were transformed into plasmids after they had invaded into E.coli BM25.8, and the E.coli clones containing the plasmids were cultured in LB medium supplemented with aminobenzylpenicillin. The isolated colonies were selected for plasmid extraction and the DNAs subsequently extracted from the plasmids underwent sequence analysis with a sequencing primer to obtain the expressed sequence tags (ESTs). After sequence editing of the resulted ESTs, comparison of these sequences with those listed in the GenBank database was performed for homology analysis. The new sequences generated from the analysis were submitted to GenBank and the accession numbers acquired. RESULTS and CONCLUSION :Altogether 58 ESTs were identified among which 3 possed highly homologous nucleotide sequences with the known genes of Sj, 2 showed the homology with Schistosoma mansori genes, 7 had the homologous protein sequences, but not the nucleotide sequences, with other species, and another 27 were poorly homologous in terms of both the nucleotide and protein sequences.

Journal Article↗

Expressed sequence tags from a root-hair-enriched medicago truncatula cDNA library

The root hair is a specialized cell type involved in water and nutrient uptake in plants. In legumes the root hair is also the primary site of recognition and infection by symbiotic nitrogen-fixing Rhizobium bacteria. We have studied the root hairs of Medicago truncatula, which is emerging as an increasingly important model legume for studies of symbiotic nodulation. However, only 27 genes from M. truncatula were represented in GenBank/EMBL as of October, 1997. We report here the construction of a root-hair-enriched cDNA library and single-pass sequencing of randomly selected clones. Expressed sequence tags (899 total, 603 of which have homology to known genes) were generated and made available on the Internet. We believe that the database and the associated DNA materials will provide a useful resource to the community of scientists studying the biology of roots, root tips, root hairs, and nodulation.

Journal Article↗

From expressed sequence tags to peroxisome biogenesis disorder genes.

Isolation of human disease genes is a challenging process and can often only be achieved by labor-intensive positional cloning techniques. Fortunately, there are alternative strategies for isolation of peroxisome biogenesis disorder genes. The first, functional complementation, was established as a viable approach by Fujiki and colleagues, who identified PAF-1, the first known peroxisome biogenesis disorder gene. The second strategy, computer-based homology probing, relies on (1) the fact that peroxisome assembly has been conserved throughout the evolution of eukaryotes, (2) knowledge of the amino acid sequences of an increasing number of yeast peroxisome assembly (PAS) genes, and (3) the existence of sequence data from large numbers of human genes. The recent development of the expressed sequence tag (EST) database (dbEST) is fulfilling the last of these requirements. We have applied the homology probing strategy in the search for candidate genes for the peroxisome biogenesis disorders by routinely screening the database of ESTs for genes with significant sequence similarity to yeast PAS genes. The validity of this approach is demonstrated by its use in identifying PXR1 as the human orthologue of the Pichia pastoris PAS8 gene and PXAAA1 as a human homologue of the Pichia pastoris PAS5 gene. Furthermore, detailed analysis of PXR1 has revealed that mutations in this gene are responsible for complementation group 2 of the peroxisome biogenesis disorders. The demonstration that human homologues of yeast PAS genes exist and that mutations in these genes cause peroxisome biogenesis disorders demonstrates that yeast pas mutants are accurate and useful models for the analysis of these diseases.

Adenosine Triphosphate↗

Mapping of 22 expressed sequence tags isolated from a porcine small intestine cDNA library.

Complementary DNA sequences were selected from a resource of tentatively identified clones from a porcine small intestine cDNA library. Forty PCR primer pairs were designed to amplify 101-309 base pairs of the 3' untranslated region of the genes. The PCR conditions were optimized by altering both formamide and magnesium concentrations on samples of pig, mouse, and hamster DNA. Twenty primer pairs that, under stringent conditions, were pig-specific and amplified the expected fragments were chosen for regional assignment in a pig/rodent hybrid cell panel. Furthermore, 22 primer pairs were chosen to amplify DNA from the parental animals of the PiGMaP shared reference families in order to detect possible polymorphisms. Primer pairs that generated polymorphisms were used for genetic mapping. A total of 22 porcine expressed sequence tags (ESTs) were cytogenetically or genetically mapped by this approach. Twelve of the mapped ESTs could be added to the human-porcine comparative map.

Animals↗