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At least 703 records · Page 39Linked to original sources
PubMed1991

Primary structure and regulation of a glucoamylase-encoding gene (STA2) in Saccharomyces diastaticus.

We have determined the complete nucleotide (nt) sequence of a 5070-bp DNA fragment containing a glucoamylase-encoding gene (STA2) from Saccharomyces diastaticus. The 5' transcription start points for STA1, STA2 and STA3 were determined by primer extension of their respective mRNAs using reverse transcriptase. The sequence data show one major open reading frame (ORF) of 767 amino acids encoding GAII with a calculated Mr of 82,514. The 5' region in the ORF contains two ATG sequences within 30 nt of each other. The upstream region of STA2 was amplified by the polymerase chain reaction (PCR) and fused to the Escherichia coli lacZ gene. Some of the PCR products contained mutations in ATG1 and/or ATG2. Results indicated that both ATG1 and ATG2 encode functional translation start codons, but ATG2 was shown to encode the stronger initiator. The upstream region of STA2 contains a canonical sequence that is homologous to known sites of repression by the MATa/MAT alpha-encoded repressor. Also, consensus RAP1 (Repressor-Activator Protein 1)-binding sites are located in the 5' upstream region and within the coding region of STA2.

Amino Acid Sequence↗
PubMed1992

Multiple protein tyrosine phosphatase-encoding genes in the yeast Saccharomyces cerevisiae.

In higher eukaryotic organisms, the regulation of tyrosine phosphorylation is known to play a major role in the control of cell division. Recently, a wide variety of protein tyrosine phosphatase (PTPase)-encoding genes (PTPs) have been identified to accompany the many tyrosine kinases previously studied. However, in the yeasts, where the cell cycle has been most extensively studied, identification of the genes involved in the direct regulation of tyrosine phosphorylation has been difficult. We have identified a pair of genes in the yeast Saccharomyces cerevisiae, which we call PTP1 and PTP2, whose products are highly homologous to PTPases identified in other systems. Both genes are poorly expressed, and contain sequence elements consistent with low-abundance proteins. We have carried out an extensive genetic analysis of PTP1 and PTP2, and found that they are not essential either singly or in combination. Neither deletion nor overexpression results in any strong phenotypes in a number of assays. Deletions also do not affect the mitotic blockage caused by deletion of the MIH1 gene (encoding a positive regulator of mitosis) and induction of the heterologous Schizosaccharomyces pombe wee1+ gene (encoding a negative regulator of mitosis). Molecular analysis has shown that PTP1 and PTP2 are quite different structurally and are not especially well conserved at the amino acid sequence level. Low-stringency Southern blots indicate that yeast may contain a family of PTPase-encoding genes. These results suggest that yeast may contain other PTPase-encoding genes that overlap functionally with PTP1 and PTP2.

Amino Acid Sequence↗
PubMed1992

A second gene (qutH) within the Aspergillus nidulans-quinic-acid utilisation gene cluster encodes a protein with a putative zinc-cluster motif.

A sequence of 3299 nt, contiguous with the previously sequenced quinate permease-encoding (qutD) gene and encompassing the dehydroshikimate dehydratase-encoding (qutC) gene, has been determined. Northern-blot analysis detected (i) a quinate-inducible mRNA of the expected size for the qutC gene, and (ii) a quinate-inducible mRNA of 1.45 kb divergently transcribed away from qutC towards qutD. Computer-aided sequence analysis identified an ORF of 1047 nt corresponding to the qutC gene encoding dehydroshikimate dehydratase. In addition, a genetically uncharacterized 1188-nt gene, designated qutH and containing a putative intron of 61 nt, was identified between qutC and qutD. The inferred protein sequence encoded by qutH contains a putative 'zinc cluster' motif and has a low (16%) but significant similarity with the DNA-directed DNA polymerase of hepatitis B virus. The results are interpreted as being consistent with the view that the qutH gene encodes a DNA-binding protein, possibly involved in the regulation of genes essential for the utilisation of protocatechuic acid.

Alcohol Oxidoreductases↗
PubMed1992

The genomic locus of the human hemopoietic-specific cell protein tyrosine kinase (PTK)-encoding gene (HCK) confirms conservation of exon-intron structure among human PTKs of the src family.

Protein tyrosine kinases (PTKs) are implicated in the control of cell growth by virtue of their frequent appearance as products of retroviral oncogenes, as intracellular signal transducers, and as growth factor receptors or components thereof. The knowledge of the structure and sequence of family genes encoding PTKs is still limited. To date, the complete genomic structure of human src family members is only available for the C-FGR gene (encoding p55 Fgr, PTK). Sequence analysis and characterization of the intron/exon organization of the human HCK gene, encoding a hemopoietic-specific cell PTK of the src-related family, revealed a length of over 16 kb for the seven 3'-exons. All intron/exon splice junctions agree with the GT/AG rule. In each case where a boundary occurs at a Gly codon, GGG or GGA, the triplet is split between the first and second nucleotide (nt). A total of eight complete and one partial Alu repeats were identified within the introns. The nt sequence of the genomic clones resolves existing discrepancies among two published sequences of HCK cDNAs. Human HCK, C-SRC (encoding p60 Src PTK), C-FGR and LCK (encoding p56 Lck, PTK) genes thus share very similar exon/intron structures for the conserved exons. These results provide additional evidence that the different PTKs of the src-like family most likely arose by duplication of an ancestral src-like gene.

Amino Acid Sequence↗
PubMed1992

Complex organization of the Streptomyces avermitilis genes encoding the avermectin polyketide synthase.

The avermectin (Av) polyketide synthase (PKS) and erythromycin (Er) PKS are encoded by modular repeats of DNA, but the genetic organization of the modules encoding Av PKS is more complex than Er PKS. Sequencing of several related DNA fragments from Streptomyces avermitilis that are part of the Av biosynthetic gene cluster, revealed that they encode parts of large multifunctional PKS proteins. The Av PKS proteins show strong similarity to each other, as well as similarity to Er PKS proteins [Donadio et al., Science 252 (1991) 675-679] and fatty acid synthases. Partial DNA sequencing of the 65-kb region containing all the related sequence elements in the avr genes provides evidence for twelve modular repeats encoding FAS-like domains. The genes encoding the Av PKS are organized as two sets of six modular repeats which are convergently transcribed.

Erythromycin↗
PubMed1992

TnblaM: a transposon for directly tagging bacterial genes encoding cell envelope and secreted proteins.

A transposon, TnblaM, designed for the direct selection of bacterial mutants with insertions in genes encoding cell envelope and secreted proteins, was constructed and subcloned into plasmid and bacteriophage lambda delivery vectors. TnblaM is a spectinomycin-resistant derivative of Tn5 with an unexpressed open reading frame encoding mature beta-lactamase (BlaM) at its left end. Therefore, when it inserts into genes in the correct orientation and reading frame, gene fusions encoding hybrid proteins are generated. By introducing TnblaM into bacterial cells and selecting ampicillin-resistant (ApR) colonies, the subset of isolates producing extracytoplasmic BlaM, and hence containing TnblaM inserted in genes encoding secreted proteins and cell envelope proteins, can be directly selected. TnblaM, like TnphoA, can therefore be used to preferentially mutagenise genes encoding extracytoplasmic proteins, but it has the advantage over TnphoA that the desired mutants can be isolated by direct selection (as ApR colonies) rather than by phenotypic screening. Isolates in which TnblaM occupies sites in the chromosome from which it can transpose at high frequency are readily identifiable, and constitute TnblaM donors, with which to simply and efficiently generate rare types of insertion mutants. Moreover, the ApR selection that is used with TnblaM can be fine-tuned to obtain blaM fusions to poorly or well-expressed genes.

Amino Acid Sequence↗
PubMed1992

Cloning and high-level expression of chitinase-encoding gene of Streptomyces plicatus.

A chitinase (Cht)-encoding gene from Streptomyces plicatus was previously cloned and expressed in Escherichia coli [Robbins et al., J. Biol. Chem., 263 (1988) 442-447]. We have sequenced this gene, compared its sequence with other genes encoding Cht and have explored its expression and regulation when reintroduced into Streptomyces lividans on multicopy plasmids. We have also cloned two other Streptomyces Cht-encoding genes and a beta-hexosaminidase-encoding gene in E. coli by expression in the lambda ZAP-Bluescript vector. The hexosaminidase and one of the Chts were expressed directly from the genomic library in E. coli at a high level as chimeric fusions with the beta-galactosidase alpha-complementing peptide encoded by the vector. Direct cloning and high-level expression of such chimeric proteins, which overcomes the difficulties associated with expressing Streptomyces genes in E. coli, should generally be possible wherever large numbers of transformants can be conveniently screened.

Amino Acid Sequence↗
PubMed1993

Cloning of a cDNA encoding a group-V (group-IX) allergen isoform from rye-grass pollen that demonstrates specific antigenic immunoreactivity.

We have isolated and characterized the cDNA clone, 19R, that encodes an isoform of a major rye-grass pollen allergen, Lol p V [previously referred to as Lol p 1b; Singh et al., Proc. Natl. Acad. Sci. USA 88 (1991) 1384-1388; and Lol p IX; Suphioglu et al., Lancet 339 (1992) 569-572]. Clone 19R was isolated from a rye-grass pollen cDNA expression library using grass pollen-specific immunoglobulin E (IgE) antibodies (Ab) from an allergic serum pool. The nucleotide (nt) sequence of clone 19R potentially encodes a 33.8-kDa protein of 339 amino acids (aa). It possesses a leader peptide essentially identical to the previously characterized isoform of Lol p V (Lol p VA). This indicates a mature processed 31.3-kDa protein of 314 aa, correlating well with the size of the polypeptides revealed by Western analysis of pollen proteins using IgE Ab affinity purified from recombinant fusion protein (reFP) encoded by clone 19R as solid matrix. There is no N-glycosylation motif. The protein encoded by clone 19R, designated Lol p VB, has 66.4% identity and 80.4% similarity with Lol p VA. However, a Lol p VA-specific monoclonal Ab, FMC A7, does not recognize reFP encoded by clone 19R, indicating that Lol p VB does not share this epitope. Cross-reactivity studies using affinity purified IgE Ab showed that both isoforms share similar allergenic epitopes. Immunoblot analysis using sera from a population of 30 patients showed that 80% possess IgE Ab that recognize both Lol p V isoforms. Variation occurred in the signal intensities of IgE binding.(ABSTRACT TRUNCATED AT 250 WORDS)

Allergens↗
PubMed1993

Analysis of the self-defense gene (fmrO) of a fortimicin A (astromicin) producer, Micromonospora olivasterospora: comparison with other aminoglycoside-resistance-encoding genes.

The nucleotide (nt) sequence of a 3409-bp PvuII fragment carrying the self-defense gene (fmrO) of a fortimicin A (FmA; astromicin) producer, Micromonospora olivasterospora, was determined; four open reading frames (ORFs) exist in this region. Expression analysis of fmrO using the lac promoter in Escherichia coli revealed that ORF-3 encodes fmrO. ORF-1 was considered to encode a FmKH epimerase (fms11). ORF-2, ORF-3 and ORF-4 seemed to form an operon. No homology was detected between fmrO and the resistance-encoding gene fmrT of Streptomyces tenjimariensis, a producer of the Fm-group antibiotic, istamycin. Gene organization around the fmr genes differed considerably between M. olivasterospora and S. tenjimariensis. The deduced amino acid sequence of fmrO showed an identity of 30.8% to grmA of M. purpurea and 35.8% to grmB of M. rosea, respectively, suggesting that fmrO encodes a 16S rRNA methyltransferase. We found in M. purpurea a novel resistance gene distinct from grmA and highly similar to fmrO which conferred a resistance phenotype similar to that of fmrO. These results suggest that fmrO of M. olivasterospora and the two resistance-encoding genes of M. purpurea were derived from a common ancestral gene.

Amino Acid Sequence↗
PubMed1995

Structure of the genes encoding the alpha- and beta-subunits of castor pyrophosphate-dependent phosphofructokinase.

Full-length genomic clones encoding the alpha- and beta-subunits of the pyrophosphate-dependent phosphofructokinase (PFP) from the castor plant have been isolated and sequenced. The gene (PFP alpha) encoding PFP alpha is approx. 5.8 kb in length and contains 19 exons, which collectively encode a protein of 617 amino acids (aa) having a deduced M(r) of 67,360. PFP beta is approx. 4.6-kb long and contains 16 exons. Together, these exons encode a protein (PFP beta), of 552 aa with a deduced M(r) of 60,114. The intron-exon splice junctions in both genes contain the consensus sequences typical for plants. An alignment of intron placement in castor PFP alpha and PFP beta with introns in the 5' portion of the gene encoding the ATP-dependent phosphofructokinase (PFK) from rabbit muscle, indicates that only one intron occupies the same position in all three genes. Furthermore, within castor PFP alpha and PFP beta, only two introns are identically placed. Within the promoter regions of castor PFP alpha and PFP beta, there are short sequences having high homology to each other (up to 65%). The results demonstrate, for the first time, that there is little homology between PFP and PFK, nor are PFP alpha and PFP beta closely related. This lack of homology suggests PFP did not evolve from PFK, but rather, that PFP and PFK have probably evolved from a common ancestral gene.

Amino Acid Sequence↗
PubMed1995

Identification of a chromosomally encoded ABC-transport system with which the staphylococcal erythromycin exporter MsrA may interact.

The energy-dependent efflux of erythromycin (Er) in staphylococci is due to the presence of msr A, which encodes an ATP-binding protein. MsrA is related to the multi-component ATP-binding cassette (ABC) transporters which characteristically also contain membrane-spanning domains. Since MsrA functions in a heterologous host in the absence of other plasmid-encoded products, the requirement for a transmembrane (TM) complex might be fulfilled by hijacking a chromosomally encoded protein. Two genes, stpA and smpA, were identified upstream from msrA on the original Staphylococcus epidermidis plasmid, encoding an ATP-binding protein and a hydrophobic TM protein, respectively. Sequences highly similar to stpA and smpA (stpB and smpB) were also found adjacent to a chromosomal copy of msrA in S. hominis. In Southern blots, internal fragments of stpA or smpA hybridized to the chromosome of the Ers S. aureus RN4220. Cloning and sequence analysis of the region identified revealed the presence of two genes, stpC and smpC, related to stpA and smpA. The deduced amino-acid sequences of the gene products showed that StpA and StpC were 85% identical, whereas SmpA and SmpC were 65% identical. A gene similar to msrA was not present in the S. aureus chromosome. There was no further sequence similarity outside these conserved regions. These results indicate that the chromosomes of S. hominis and S. aureus contain sequences encoding a potential TM protein with which MsrA might interact.

Amino Acid Sequence↗
PubMed1994

Differential CNS expression of alternative mRNA isoforms of the mammalian genes encoding cAMP-specific phosphodiesterases.

To study alternative splicing and tissue-specific expression of the mammalian genes encoding type-IV cAMP-specific phosphodiesterases, which are homologs of the dnc learning and memory gene of Drosophila melanogaster, we cloned seven cDNAs from four rat loci (PDE1, PDE2, PDE3 and PDE4) homologous to dnc. The deduced amino-acid sequences of the proteins encoded by the rat loci were shown to have a 1:1 correspondence with those encoded by the four human dnc homologs. The proteins encoded by at least one cDNA from each of the four rat loci contained novel N-terminal upstream conserved regions (UCR1 and UCR2), described previously in proteins encoded by the human dnc homologs and by dnc. cDNAs from three of the rat loci (PDE2, PDE3 and PDE4) had a structure consistent with alternative splicing of the 5' coding regions of their respective mRNAs. UCR1, and in one case a portion of UCR2, were absent in one of the alternatively spliced transcripts from these three loci. RNase protection analysis showed that the rat PDE3 and PDE4 loci were each expressed at relatively constant levels in multiple regions of the brain, while PDE2 transcripts were more abundant in temporal cortex and brainstem. One of the alternatively spliced mRNAs from the PDE4 locus was relatively more abundant in temporal cortex and cerebellum. One alternatively spliced transcript from the PDE3 locus was expressed more abundantly in parietal cortex. Both of the alternatively spliced transcripts from the human DPDE4 locus (the homolog of rat PDE4) were expressed in temporal cortex.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed1994

Cloning and characterization of a yeast cytochrome b5-encoding gene which suppresses ketoconazole hypersensitivity in a NADPH-P-450 reductase-deficient strain.

Cytochrome P-450 (Cyp) 51 or lanosterol-C14-demethylase is the main target for antifungal compounds of the triazole family like ketoconazole (Kz). Disruption of the associated NADPH-P-450 reductase-encoding gene (YRED) is not lethal, but decreases by about 20-fold the Kz resistance (KzR) of wild-type (wt) Saccharomyces cerevisiae. Transformation of a YRED-disrupted strain by a yeast genomic library based on a multicopy vector allowed us to identify a suppressor of Kz hypersensitivity. Deletion analysis of the 5-kb cloned fragment indicated that yeast cytochrome b5-encoding gene (CYB5), which encodes a 120-amino-acid (aa) protein, is required and sufficient for the suppressor effect. The encoded polypeptide shares about 30% aa identity with mammalian cytochromes b5 (Cyb5). CYB5 disruption and tetrad analysis demonstrate that yeast Cyb5 is not required for growth in a Yred+ strain. Determination of the microsomal content of b-type cytochromes by differential spectra indicated the presence of a strongly decreased or null Cyb5 level in the disrupted strain. This confirms that we have cloned the gene encoding the major microsomal form of Cyb5 which appears not to be essential. Minor Cyb5 isoforms could also be present in yeast or other redox proteins could substitute for the pleiotropic roles of Cyb5 in the sterol and lipid biosynthesis pathways.

Amino Acid Sequence↗
PubMed1994

Construction and expression in Escherichia coli of hybrid genes composed of sequences encoding diphtheria toxin and human CD4 receptor.

Derivatives of natural toxins possessing substituted receptor-recognition domains of different specificities can be used as instruments for the selective elimination of target cells. We have constructed two different types of hybrid genes that encode proteins composed of diphtheria toxin (DT) lacking the C-terminal residues that mediate toxin binding fused with the N-terminal region of human CD4 (Lys10 to Glu152). One of these hybrids encodes a protein with CD4 at the N terminus, while the other encodes a protein with CD4 at the C terminus. The stability of these two proteins was dramatically different. We could not detect a full-size product when the first construct was expressed in Escherichia coli. In contrast, proteins encoded by the second construct were more stable. In the latter case, the amount of full-size hybrid protein was 1-2% of the total cell protein. We speculate on the involvement of the region that resembles the processing site of Pseudomonas aeruginosa exotoxin A in the proteolytic degradation of the product encoded by the first type of hybrid.

Amino Acid Sequence↗
PubMed1995

Lens epithelial cell mRNA, II. Expression of a mRNA encoding a lipid-binding protein in rat lens epithelial cells.

A lens epithelial (LE) cell cDNA clone, designated pLELBP, was isolated by subtraction-hybridization methods between a 4-week-old rat LE cell and rat lens fiber cell lambda ZAP cDNA libraries. The cDNA contained 683 bp, an ATG at bp 42, and an open reading frame (ORF) encoding a protein of 135 amino acids (aa), and a poly(A) signal at bp 641 (GenBank/EMBL accession No. U13253). Northern blot analysis showed that the lens mRNA was at a concentration that exceeded 100-fold that found in non-ocular tissues examined, except in skin it was found at levels equal to about 1/15 of the lens levels. In the retina, it was also found at about 1/15 of that present in the lens. By in situ hybridization analysis, the sense RNA was localized to the LE cells and to the glial cells of the retina, and negligibly to the lens fiber cells. Search of GenBank, EMBL and SwissProt data bases revealed that the LE cell mRNA and its aa encoded protein showed extensive sequence homology to members of the cytosolic lipid-binding protein (LBP) family. It matched to 91% in aa sequence homology to the protein encoded by ORF of mal1 cDNA, isolated from mouse skin squamous cell carcinoma [Krieg et al., J. Biol. Chem. 268 (1993) 17362-17369], and 99% in aa sequence homology to the protein encoded by ORF of rat skin LBP mRNA [Watanabe et al., Biochem. Biophys. Res. Commun. 200 (1994) 253-259]. Occurrence of high levels of mRNA for a specific LBP in the LE cells relative to other non-ocular tissues is consistent with a hypothesis that the encoded protein may be involved in several lens epithelial cell-specific mechanisms, possibly including differentiation, protective and nutritional processes.

Animals↗
PubMed1996

Analysis of the human gene encoding latent transforming growth factor-beta-binding protein-2.

Transforming growth factor (TGF)-beta is secreted as an inactive complex, which frequently contains a large molecular weight binding protein designated latent TGF-beta-binding protein (LTBP). Recently, the LTBPs have been shown to be a gene family that contains three known members and exhibits a multidomain structure containing cysteine-rich motifs that are also found in the fibrillin gene family. The present work seeks to characterize the gene encoding LTBP-2 and to compare its features to that of the other LTBPs and to the fibrillins. Human fibroblast libraries were used to isolate cDNA encoding LTBP-2 which was then used to identify LTBP-2 transcripts and to isolate the corresponding LTBP-2 gene. The cloned cDNA encodes a 195 kDa protein containing 20 epidermal growth factor (EGF)-like repeats, three repeats containing eight cysteines, and one segment that appears to be a hybrid of the two. Single exons encode EGF repeats while the eight-cysteine repeats are encoded in two exons. Northern analysis identified two transcripts of 7.5 and 9.0 kb, with the presently analyzed cDNA probably corresponding to the 7.5 transcript. Phylogenetic sequence comparisons demonstrated that LTBP-3 is more similar to LTBP-1 than LTBP-2, while LTBP-2 shows the most similarity to the fibrillins. These analyses suggest that LTBP-1 diverged from LTBP-3, and that LTBP-2 diverged from LTBP-1. Within the fibrillin family, fibrillin-1 is nearest to the LTBPs. While the domain structure of LTBP-2 is similar to that of the other LTBPs, LTBP-2 possesses unique regions that make it the largest member of the LTBP family. LTBP-2 may have dual functions as a member of the TGF-beta latent complex and as a structural component of microfibrils.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Anterior medial temporal lobe activation during encoding of words: FMRI methods to optimize sensitivity.

The existence of a rostrocaudal gradient of medial temporal lobe (MTL) activation during memory encoding has historically received support from positron emission tomography studies, but less so from functional MRI (FMRI) studies. More recently, FMRI studies have demonstrated that characteristics of the stimuli can affect the location of activation seen in the MTL when those stimuli are encoded. The current study tested the hypothesis that MTL activation during memory encoding is related to the modality of stimulus presentation. Subjects encoded auditorily or visually presented words in an FMRI novelty paradigm. Imaging and analysis parameters were optimized to minimize susceptibility artifact in the anterior MTL. Greater activation was observed in the anterior than posterior MTL for both modalities of stimulus presentation. The results indicate that anterior MTL activation occurred during encoding, independent of stimulus modality and provide support for the hypothesis that verbal-semantic memory processing occurs in anterior MTL. The authors suggest that technical factors are critical for observing the rostrocaudal gradient in MTL memory activation.

Acoustic Stimulation↗
PubMed2007

The neural representation of odor is modulated by the presence of a trigeminal stimulus during odor encoding.

OBJECTIVES: Odor perception does not simply consist in hierarchical processing from transduction to a single "true" cerebral representation. Odor sensation may be modulated by available sensory information during encoding. The present study set out to examine whether the presence of a pure trigeminal stimulus during odor encoding may modulate odor perception at both behavioral and cortical levels. METHODS: Participants were tested in a 2-session within-subject design: first, an odor encoding session included a delay conditioning procedure in which relatively selective olfactory stimulants (phenyl ethyl alcohol or vanillin, Conditioned Stimulus+, CS+) were presented either with a pulse of CO(2) (Unconditioned Stimulus, US), or alone (Conditioned Stimulus-, CS-); then, in the second session, both pure odorants (CS+ and CS-) were presented alone. During this second session, olfactory event-related potentials were simultaneously recorded and analyzed at different electrode sites including Cz and Pz (sites known to have maximal amplitudes for trigeminal and olfactory stimuli, respectively). After each trial, subjects were asked to rate odor intensity and hedonics. RESULTS: The results showed that CS+ intensity ratings increased in 8 subjects and decreased in 6. Cortically, a group effect was observed for P2 amplitude, which increased in the "CS+ intensity increase" group vs. the "CS+ intensity decrease" group at Cz (p<0.05) but not at Pz (p>0.05). CONCLUSIONS: This result suggests that the presence of a pure trigeminal stimulus (CO(2)) during odor encoding alters the neural representation of a pure odor. SIGNIFICANCE: The neural representation of odors comprises not only the odor itself but also contextual information (trigeminal in the present case) presented during encoding.

Adult↗