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At least 1,153 records · Page 64Linked to original sources
PubMed1995

Identification of a cDNA that encodes a 1-acyl-sn-glycerol-3-phosphate acyltransferase from Limnanthes douglasii.

Two different techniques were used to isolate potential cDNAs for acyl-CoA: 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPA-AT) enzymes from Limnanthes douglasii. Both heterologous screening with the maize pMAT1 clone and in vivo complementation of the Escherichia coli mutant JC201 which is deficient in LPA-AT activity, were carried out. Clones identified by these procedures were different. Homology searches demonstrated that the clone isolated by heterologous probing, pLAT1, encodes a protein which is most similar to the maize (open reading frame in pMAT1) and yeast SLC1 proteins, which are putative LPA-AT sequences. This L. douglasii sequence shows much lower homology to the E. coli LPA-AT protein PlsC, which is the only LPA-AT sequence confirmed by over-expression studies. The clone isolated by complementation, pLAT2, encodes a protein with homology to both SLC1 and PlsC. It was not possible to over-express the complementing protein encoded by pLAT2 but further experimentation on membranes from complemented JC201 demonstrated that they possess a substrate specificity distinctly different from PlsC and similar to Limnanthes sp. microsome specificity. This data strongly supports the contention that pLAT2 is an LPA-AT clone. Northern blot analysis revealed different expression patterns for the two genes in pLAT1 and pLAT2. Transcription of the gene encoding the insert of pLAT2 occurred almost exclusively in developing seed tissue, whilst the cDNA of pLAT1 hybridised to poly(A)+ mRNA from seed, stem and leaf, demonstrating more widespread expression throughout the plant. Southern blot analysis indicated that the cDNA of pLAT2 was transcribed from a single-copy gene while that for pLAT1 was a member of a small gene family.

1-Acylglycerol-3-Phosphate O-Acyltransferase↗
PubMed1994

Cloning and nucleotide sequence of a cDNA encoding a major fucoxanthin-, chlorophyll a/c-containing protein from the chrysophyte Isochrysis galbana: implications for evolution of the cab gene family.

We investigated the primary structure of a cDNA encoding a light-harvesting protein from the marine chrysophyte Isochrysis galbana. Antibodies raised against the major fucoxanthin, chlorophyll a/c-binding light-harvesting protein (FCP) of I. galbana were used to select a cDNA clone encoding one of the FCP apoproteins. The nucleic acid and deduced amino acid sequences reveal conserved regions within the first and third transmembrane spans with Chl a/b-binding proteins and with FCPs of another chromophyte. However, the amino acid identity between I. galbana FCP and other cab genes of FCPs is only ca. 30%. Phylogenetic analyses demonstrated that the FCP genes of both diatoms and chrysophytes sequenced to date are more closely related to cab genes encoding LHC I, CP 29, and CP 24 of higher plants than to cab genes encoding LHC II of chlorophytes. We propose that LHC I, CP 24 and CP 29 and FCP might have originated from a common ancestral chl binding protein and that the major LHC II of Chl a/b-containing organisms arose after the divergence between the chromophytes and the chlorophytes.

Amino Acid Sequence↗
PubMed1994

Repetitive activity of a branched Hodgkin-Huxley axon with multiple encoding sites.

Afferent activity in a receptor afferent fiber with several encoding sites is generally believed to represent the activity of the fastest pacemaker that resets all more slowly encoding sites. Alternatively, some impulse mixing as well as some nonlinear summation of receptor current to a single encoder have been considered. In this article the repetitive firing activity of a Hodgkin-Huxley axon consisting of two branches that join into a single stem axon was investigated. The model axon was stimulated by constant-current injection into either the right or the left or both branches. It was found that the model axon generated an (infinite) train of action potentials if the input current was large enough. The discharge frequency found was constant, and on combined stimulation of both branches with different current, the site of impulse initiation was always in the branch receiving the higher input current, excluding a simple impulse mixing. On the other hand, the combined stimulation of both branches evoked repetitive firing with a higher frequency than expected by the pacemaker-resetting hypothesis. Moreover, a stimulus that is subthreshold for repetitive firing if injected into one branch yields repetitive firing when it is injected into both branches, a behavior inconsistent with impulse mixing and pacemaker resetting. On the other hand, current injection into one branch allowed repetitive activity only within a rather limited range of firing frequencies. Using distributed current injection into both branches, however, allowed many more different firing frequencies. Such behavior is inconsistent with both pacemaker resetting and (nonlinear) input current summation. Consequently, the repetitive firing behavior of a branched Hodgkin-Huxley axon with multiple encoding sites appears to be more complex than postulated in the simple hypotheses.

Action Potentials↗
PubMed1993

Cloning and sequence analysis of cDNAs encoding the MHC class II beta chain in Atlantic salmon (Salmo salar).

Atlantic salmon (Salmo salar) cDNAs encoding the major histocompatibility complex (Mhc-Sasa) class II beta chain were isolated from a leucocyte library by a polymerase chain reaction (PCR) approach. Three different cDNAs (c144, c22, and c157) encoding the entire mature beta chain have been analyzed. Clone c144 differs from clone c157 in 12.6% of the nucleotides in the beta 1-encoding region. The corresponding differences between clones c144 and c22, and clones c22 and c157, are 10.3% and 5.2%, respectively. This variation is, at least in part, most likely attributable to allelism. The similarity indices between the highly conserved beta 2 domains from Atlantic salmon and corresponding sequences from humans (DQ beta), chicken (BL beta), carp (TLAII beta-1), and rainbow trout (O.M. No. 55) are 45%, 40%, 66%, and 97%, respectively. Variable residues in the beta 1 domains from Atlantic salmon correspond with polymorphic sites of beta 1 domains from higher vertebrates. The frequency of substitutions in the beta 1-encoding region exceeds that in the 3'-untranslated (UT) region with several folds, indicating extensive beta 1 polymorphism in Atlantic salmon.

Amino Acid Sequence↗
PubMed1990

Identification of mRNA that encodes an alternative form of H-CAM(CD44) in lymphoid and nonlymphoid tissues.

The cluster of differentiation 44 (CD44), hereafter referred to as H-CAM(CD44), represents a novel class of polymorphic (Mr 80,000-215,000) cell adhesion molecules that are involved in cell-cell and cell-matrix adhesion events in a variety of organ systems. We report the detection of distinct mRNAs, in both hematopoietic and nonhematopoietic human cell lines, that encode H-CAM(CD44) with different cytoplasmic domains. Genomic Southern blot analyses indicate that the exons encoding these two cytoplasmic domains are located on the same approximately 16 kilobase (kb) Eco RI restriction fragment. Restriction endonuclease and Southern blot analyses performed on polymerase chain reaction (PCR) amplification copies of these mRNAs confirm that their sequences correspond with previously reported cDNA sequences. A consensus splice donor site which is conserved in human, baboon, and mouse mRNAs that encode a molecule with an elongated cytoplasmic domain (H-CAM-L) is utilized to generate a distinct but low-abundance mRNA species that encodes H-CAM(CD44) with a truncated cytoplasmic domain of only three amino acids (H-CAM-S). Estimations of the relative abundance of these mRNA species in B-lymphoblastoid cells using the PCR amplification technique exhibit average H-CAM-L/H-CAM-S ratios ranging between 100 and 200. Therefore, H-CAM (CD44)-mediated adhesive events may be regulated through a differential capacity of H-CAM-L and H-CAM-S to interact with the cytoskeleton and to participate in intracellular signaling events.

Base Sequence↗
PubMed1990

Analysis of a cDNA encoding arginine decarboxylase from oat reveals similarity to the Escherichia coli arginine decarboxylase and evidence of protein processing.

Arginine decarboxylase is the first enzyme in one of the two pathways of putrescine synthesis in plants. We purified arginine decarboxylase from oat leaves, obtained N-terminal amino acid sequence, and then used this information to isolate a cDNA encoding oat arginine decarboxylase. Comparison of the derived amino acid sequence with that of the arginine decarboxylase gene from Escherichia coli reveals several regions of sequence similarity which may play a role in enzyme function. The open reading frame (ORF) in the oat cDNA encodes a 66 kDa protein, but the arginine decarboxylase polypeptide that we purified has an apparent molecular weight of 24 kDa and is encoded in the carboxyl-terminal region of the ORF. A portion of the cDNA encoding this region was expressed in E. coli, and a polyclonal antibody was developed against the expressed polypeptide. The antibody detects 34 kDa and 24 kDa polypeptides on Western blots of oat leaf samples. Maturation of arginine decarboxylase in oats appears to include processing of a precursor protein.

Amino Acid Sequence↗
PubMed1991

Evolutionary conservation of the chlorophyll a/b-binding proteins: cDNAs encoding type I, II and III LHC I polypeptides from the gymnosperm Scots pine.

cDNAs encoding three different LHC I polypeptides (Type I, Type II and Type III) from the gymnosperm Scots pine (Pinus sylvestris L.) were isolated and sequences. Comparisons of the deduced amino acid sequences with the corresponding tomato sequences showed that all three proteins were highly conserved although less so than the LHC II proteins. The similarities between mature Scots pine and tomato Types I, II and III LHC I proteins were 80%, 87% and 85%, respectively. Two of the five His residues that are found in AXXXH sequences, which have been identified as putative chlorophyll ligands in the Type I and Type II proteins, were not conserved. The same two regions of high homology between the different LHC proteins, which have been identified in tomato, were also found in the Scots pine proteins. Within the conserved regions, the Type I and Type II proteins had the highest similarity; however, the Type II and Type III proteins also showed a similarity in the central region. The results suggest that all flowering plants (gymnosperms and angiosperms) probably have the same set of LHC polypeptides. A new nomenclature for the genes encoding LHC polypeptides (formerly cab genes) is proposed. The names lha and lhb are suggested for genes encoding LHC I and LHC II proteins, respectively, analogous to the nomenclature for the genes encoding other photosynthetic proteins.

Amino Acid Sequence↗
PubMed1992

Isolation and phenotypic analysis of conditional-lethal, linker-insertion mutations in the gene encoding the largest subunit of RNA polymerase II in Saccharomyces cerevisiae.

Linker-insertion mutagenesis was used to isolate mutations in the Saccharomyces cerevisiae gene encoding the largest subunit of RNA polymerase II (RPO21, also called RPB1). The mutant rpo21 alleles carried on a plamid were introduced into a haploid yeast strain that conditionally expresses RPO21 from the inducible promoter pGAL10. Growth of this strain on medium containing glucose is sustained only if the plasmid-borne rpo21 allele encodes a functional protein. Of nineteen linker-insertion alleles tested, five (rpo21-4 to -8) were found that impose a temperature-sensitive (ts) lethal phenotype on yeast cells. Four of these five ts alleles encode mutant proteins in which the site of insertion lies near one of the regions of the largest subunit that have been conserved during evolution. Two of the ts mutants (rpo21-4 and rpo21-7) display pleiotropic phenotypes, including an auxotrophy for inositol and a decreased proliferation rate at the permissive temperature. The functional relationship between RPO21 and RPO26, the gene encoding the 17.9 kDa subunit shared by RNA polymerases I, II, and III was investigated by determining the ability of increased dosage of RPO26 to suppress the ts phenotype imposed by rpo21-4 to -8. Suppression of the ts defect was specific for the rpo21-4 allele and was accompanied by co-suppression of the inositol auxotrophy. These results suggest that mutations in the largest subunit of RNA polymerase II can have profound effects on the expression of specific subsets of genes, such as those involved in the metabolism of inositol. In the rpo21-4 mutant, these pleiotropic phenotypes can be attributed to a defective interaction between the largest subunit and the RPO26 subunit of RNA polymerase II.

Alleles↗
PubMed1990

Detection of a protein encoded by a class II mitochondrial intron of Podospora anserina.

In the filamentous fungus Podospora anserina, the amplification as circular DNA molecules of the first intron (intron alpha) of the CO1 mitochondrial gene, encoding the cytochrome oxidase subunit 1, is known to be strongly associated with aging of strains. In this study we have attempted to detect the protein potentially encoded by the open reading frame (ORF) contained in this intron. This was done by the Western blot technique using specific antisera raised against three polypeptides encoded by three non-overlapping fragments of this ORF adapted to the universal code and overexpressed in Escherichia coli. We examined about thirty independent subclones of Podospora derived from two different geographic races (A, s), using wild-type and mutant strains, young and senescent cultures. A 100 kDa polypeptide, encoded by the class II intron alpha, was detected in five senescent subclones which all showed strong amplification of the intronic alpha sequence (Sen DNA alpha).

Cloning, Molecular↗
PubMed1993

Molecular analysis of the gene encoding a rice starch branching enzyme.

The sequence of a rice gene encoding a starch branching enzyme (sbe1) shows extreme divergence from that of the rice gene, that is homologous to bacterial glycogen branching enzyme (sbe2). sbe1 is expressed abundantly and specifically in developing seeds and maximally in the middle stages of seed development. This expression pattern completely coincides with that of the waxy gene, which encodes a granule-bound starch synthase. Three G-box motifs and consensus promoter sequences are present in the 5' flanking region of sbe1. It encodes a putative transit peptide, which is required for transport into the amyloplast. A 2.2 kb intron (intron 2) precedes the border between the regions encoding the transit peptide and the mature protein, and contains a high G/C content with several repeated sequences in its 5' half. Although only a single copy of sbe1 is present in the rice genome, Southern analysis using intron 2 as a probe indicates the presence of several homologous sequences in the rice genome, suggesting that this large intron and also the transit peptide coding region may be acquired from another portion of the genome by duplication and insertion of the sequence into the gene.

1,4-alpha-Glucan Branching Enzyme↗
PubMed1992

Characterisation of actI-homologous DNA encoding polyketide synthase genes from the monensin producer Streptomyces cinnamonensis.

Cloned DNA encoding polyketide synthase (PKS) genes from one Streptomyces species was previously shown to serve as a useful hybridisation probe for the isolation of other PKS gene clusters from the same or different species. In this work, the actI and actIII genes, encoding components of the actinorhodin PKS of Streptomyces coelicolor, were used to identify and clone a region of homologous DNA from the monensin-producing organism S. cinnamonensis. A 4799 bp fragment containing the S. cinnamonensis act-homologous DNA was sequenced. Five open reading frames (ORFs 1-5) were identified on one strand of this DNA. The five ORFs show high sequence similarities to ORFs that were previously identified in the granaticin, actinorhodin, tetracenomycin and whiE PKS gene clusters. This allowed the assignment of the following putative functions to these five ORFS: a heterodimeric beta-ketoacyl synthase (ORF1 and ORF2), an acyl carrier protein (ORF3), a beta-ketoacyl reductase (ORF5), and a bifunctional cyclase/dehydrase (ORF4). The ORFs are encoded in the order ORF1-ORF2-ORF3-ORF5-ORF4, and ORFs-1 and -2 show evidence for translational coupling. This act-homologous region therefore appears to encode a PKS gene cluster. A gene disruption experiment using the vector pGM160, and other evidence, suggests that this cluster is not essential for monensin biosynthesis but rather is involved in the biosynthesis of a cryptic aromatic polyketide in S. cinnamonensis. An efficient plasmid transformation system for S. cinnamonensis has been established, using the multicopy plasmids pWOR120 and pWOR125.

Amino Acid Sequence↗
PubMed1990

Transcriptional analysis of the DD-peptidase/penicillin-binding protein-encoding dac gene of Streptomyces R61: use of the promoter and signal sequences in a secretion vector.

The promoter region of the gene encoding the extracellular DD-peptidase/penicillin-binding protein of Streptomyces R61 has been identified by in vivo promoter probing and S1 mapping. A secretion vector, pDML116, was constructed by inserting into the multicopy Streptomyces plasmid pIJ702, a 247 bp DNA sequence that contained the transcriptional, translational and secretory signals and the 12 amino acid N-terminal region-encoding sequence of the mature Streptomyces DD-peptidase/penicillin-binding protein. Insertion, downstream of this 247 bp segment, of the Streptomyces R61 DD-peptidase-encoding gene or the Escherichia coli R-TEM beta-lactamase-encoding gene yielded plasmids pDML120 and pDML128, respectively, which allowed expression and secretion of the relevant enzymes by Streptomyces lividans. The maximal secretion levels obtained were 42 mg protein/ml for the autologous Streptomyces DD-peptidase and 0.9 mg protein/ml for the heterologous E. coli beta-lactamase.

Amino Acid Sequence↗
PubMed1989

Identification and characterization of the genes encoding three structural proteins of the Thermoproteus tenax virus TTV1.

Three structural proteins, TP1, TP2 and TP3, of the virus TTV1 of the thermophilic archaebacterium Thermoproteus tenax strain Kra1 were mapped within the viral genome by locating the amino-terminal amino acid sequences of these proteins in the TTV1 DNA sequence. The derived amino acid sequences comprise 113, 139 and 160 amino acid residues, respectively. All three proteins are hydrophobic. The three genes are not linked, but transcribed in the same direction. No Shine-Dalgarno sequences are found in the vicinity of the initiation codons of these three genes. By Northern analysis, four mRNAs of 0.5 kb, 0.8 kb, 1.1 kb and 1.8 kb in size were found to be encoded in the region and in the vicinity of the genes, the shortest one (t1) encoding TP3 and the longest one (t4) encoding TP2. No transcript from the region encoding TP1 has been found so far. A transcriptional start site was mapped for the transcript t1. Its upstream sequence was similar to the putative consensus sequence for archaebacterial promoters.

Amino Acid Sequence↗
PubMed1988

Comparative analysis of genes encoding methyl coenzyme M reductase in methanogenic bacteria.

The sequence of the gene cluster encoding the methyl coenzyme M reductase (MCR) in Methanococcus voltae was determined. It contains five open reading frames (ORF), three of which encode the known enzyme subunits. Putative ribosome binding sites were found in front of all ORFs. They differ in their degrees of complementarity to the 3' end of the 16 S rRNA, which is discussed in terms of different translation efficiencies of the respective genes. The codon usage bias is different in the subunit encoding genes compared with the two other ORFs in the cluster and two other known genes of Mc. voltae. This is interpreted in terms of increased translational accuracy of the highly expressed MCR subunit genes. The derived polypeptide sequences encoded by the five ORFs of the MCR cluster were compared to those of the respective genes in Methanobacterium thermoautotrophicum Marburg and Methanosarcina barkeri. Conserved regions were detected in the enzyme subunits, which are candidates for factor binding domains. Conserved hydrophobic sequences found in the alpha and beta subunits are discussed with respect to the membrane association of the enzyme.

Amino Acid Sequence↗
PubMed1984

Antigen-specific helper T cells recognize determinants encoded in the H-2D region of the H-2 gene complex.

Observations have frequently been interpreted as showing that the helper T cells which collaborate with alloantigen-specific cytotoxic T-cell precursors can only recognize antigens encoded in the I region of the H-2 gene complex. An experimental system is described here that allows analysis of the recognition repertoire of these helper cells. CBA helper T-cell precursors can be primed in vitro to antigens encoded in the H-2b gene complex. These helpers can then be tested for the existence of a subset of helper cells which recognize antigens encoded in the D region of H-2b haplotype. CBA thymocytes were used as a source of cytotoxic T-cell precursors that respond poorly in the absence of exogeneous helper activity. The source of alloantigen was varied by using irradiated spleen cells from various (BALB/c X recombinant)F1 hybrid mice as stimulator cells. When the stimulator cell bears BALB/c determinants recognized by the cytotoxic T-cell precursor and also bears only the D region antigens of the H-2b haplotype, an anti-BALB/c cytotoxic response is generated only if the anti-H-2b helper population contains cells able to recognize H-2Db. A positive cytotoxic response was obtained, indicating that helper cells are not limited to recognition of I region antigens and can efficiently recognize antigens encoded in the D region of the H-2 gene complex. This was confirmed by the demonstration of helpers specific for H-2Dd. We were unable to detect any evidence for Ia-restricted recognition of the H-2D alloantigens, suggesting that, as for cytotoxic T lymphocytes (CTL), helper cell recognition of class I alloantigens is an unrestricted event.

Animals↗
PubMed1988

A third class I major histocompatibility complex antigen encoded by a gene in the D region of the H-2d haplotype recognized by cytotoxic T lymphocytes.

The D region of the H-2d haplotype contains five class I genes: H-2Dd, D2d, D3d, D4d and H-2Ld. Although previous studies have suggested the presence of D-end encoded class I molecules in addition to H-2Dd and H-2Ld, segregation of genes encoding such molecules has not been demonstrated. In this report we have used cytotoxic T lymphocytes (CTL) to examine the D region of the H-2d haplotype for the presence of additional class I molecules. CTL generated in (C3H x B6.K1)F1 (KkDk, KbDb) mice against the hybrid class I gene product Q10d/Ld expressed on L cells cross-react with H-2Ld but not H-2Dd molecules, as determined by lysis of transfected cells expressing H-2Ld but not H-2Dd. Although H-2Ld-specific monoclonal antibodies (mAb) completely inhibit H-2Ld-specific CTL from killing B10.A(3R) (KbDdLd) target cells, only partial inhibition of anti-Q10 CTL-mediated lysis was observed, suggesting the presence of an additional D-end molecule as a target for these latter CTL. To identify the region containing the gene encoding the Q10 cross-reactive molecule, we show that anti-Q10 CTL lyse target cells from a D-region recombinant strain B10.RQDB, which has H-2Dd, D2d, D3d, D4d, and H-2Db but not the H-2Ld H-2d, and H-2Ld (including D2d, D3d, and D4d), lacks this anti-Q10 CTL target molecule. Together, these data demonstrate that a class I gene mapping between H-2Dd and H-2Ld encodes an antigen recognized by anti-Q10 CTL. A likely candidate for this gene is D2d, D3d, or D4d.

Animals↗
PubMed1982

A model for impulse frequency modulation used in neural encoding.

The impulse rate at the output of a neural encoder can be interpreted as the sum of the mean impulse rate plus a noise component. From literature models are known which describe the transient phenomena of the encoder as far as the mean impulse rate is concerned. In this paper in addition the noise phenomenon is treated by a model which is in agreement with results derived from measurements. This model consists of two parts, a multiplicative and an additive estimator. The first one is similar to the automatic gain control system known from literature. This system estimates the amplification of the impulse rate due to the step input of the neural encoder. Multiplying the impulse rate with the inverse of this factor inhibits the change of the impulse rate. The second estimator calculates the step size of the impulse rate which is subtracted from the output of the encoder. Again the change of the impulse rate is inhibited. The comparison of the impulse rates simulated by the model and given by published measurements shows a good agreement for the properties of the mean impulse rate and the variance of the imposed noise.

Animals↗
PubMed1996

Sequence analysis of a Molluscum contagiosum virus DNA region which includes the gene encoding protein kinase 2 and other genes with unique organization.

The nucleotide sequence of a near left-terminal region from the genome of Molluscum contagiosum virus subtype I (MCVI) was determined. This region was contained within three adjacent BamHI fragments, designated L (2.4 kilobases (kb)), M (1.8 kb), and N (1.6 kb). BamHI cleavage of MCVI DNA produced another 1.6-kb fragment (N'), which had been mapped 30-50 kb from the L,M region. The MCVI restriction fragments were cloned and end-sequenced. The N fragment that maps at the L,M region was identified by the polymerase chain reaction, using primers devised from the sequence of each fragment. The results from this analysis led to establish the relative position of these fragments within the MCVI genome. The analysis of 3.6 kb of DNA sequence revealed the presence of ten open reading frames (ORFs). Comparison of the amino acid sequence of these ORFs to the amino acid sequence of vaccinia virus (VAC) proteins revealed that two complete MCVI ORFs, termed N1L and L1L, showed high degree of homology with VAC F9 and F10 genes, respectively. The F10 gene encodes a 52-kDa serine/threonine protein kinase (protein kinase 2), an essential protein involved in virus morphogenesis. The MCVI homologue (L1L) encoded a putative polypeptide of 443 aa, with a calculated molecular mass of 53 kDa, and 60.5/30.2% sequence identity/similarity to VAC F10. The MCV N1L (213 aa, 24 kDa) showed 42.6/40.6% amino acid sequence identity/similarity to VAC F9, a gene of unknown function encoding a 24-kDa protein with a hydrophobic C-terminal domain, which was conserved in MCVI. The genomic arrangement of MCVI N1L and L1L was equivalent to that of the vaccinia and variola virus homologues. However, the ORFs contained within MCVI fragment M (leftward) showed no homology, neither similarity in genetic organization, to the genes encoded by the corresponding regions of vaccinia and variola viruses.

Amino Acid Sequence↗