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At least 703 records · Page 39Linked to original sources
PubMed2004

Pelargonium necrotic spot virus: a new member of the genus Tombusvirus.

A virus isolate from Pelargonium spp., provisionally designated UPEV (unknown pelargonium virus), had isometric particles 31-33 nm in diameter, with a granular surface structure similar to that of viruses in three genera of family Tombusviridae. Immunoelectron microscopy proved that UPEV was serologically distinct from all examined morphologically similar members of the family Tombusviridae. The induced cytopathology was characterized by large cytoplasmic virion aggregates and the formation of multivesicular bodies derived from mitochondria. Analysis of the complete ssRNA genome sequence revealed four open reading frames (ORFs) arranged like those of viruses in the genera Tombusvirus and Aureusvirus. Sequence comparisons indicated that three of the four ORFs had a high identity (52-97% identical amino acids) with the respective ORFs of tombusvirus species, especially with Carnation Italian ringspot virus, but not with those of viruses in other genera in Tombusviridae. On the contrary, UPEV coat protein had a low indentity (36-53% identical amino acids) with that of the aureusvirus Pothos latent virus. The data suggested that UPEV originated in a recombination event between a tombus- and an aureusvirus. According to its original host and symptom expression we proposed the new virus be named Pelargonium necrotic spot virus (PeNSV) and classified it as a distinct and new species in the genus Tombusvirus.

Capsid Proteins↗
PubMed1999

Cloning of a second proopiomelanocortin cDNA from the pituitary of the sturgeon, Acipenser transmontanus.

A recent study on the pituitary of the sturgeon, Acipenser transmontanus, resulted in the cloning of a cDNA that codes for the prohormone, proopiomelanocortin (POMC). This cDNA is designated sturgeon POMC A. Subsequent analysis of the sturgeon pituitary uncovered a second distinct POMC cDNA (sturgeon POMC B). In both sturgeon POMC cDNAs the open reading frame is 795 nucleotides in length. However, the two sturgeon POMC cDNAs differ at 26 amino acid positions in the opening frame. In addition, the 2 forms of POMC differ at 45 nucleotide positions within the open reading frame. The number and types of point mutations are compared in the 2 sturgeons POMC cDNAs, and the origin of the two POMC genes is discussed.

Amino Acid Sequence↗
PubMed1999

Novel endothelin B receptor transcripts with the potential of generating a new receptor.

Using RT-PCR and rapid amplification of 5' cDNA ends (5' RACE), we have cloned three previously unrecognized endothelin B receptor (EDNRB) transcripts from a human melanoma cell line. Three distinct types of cDNAs (EDNRBDelta1, Delta2 and Delta3) were identified. EDNRBDelta1 starts upstream of the published transcription start site of hEDNRB without splicing, whereas, EDNRBDelta2 and EDNRBDelta3 are alternatively spliced. EDNRBDelta1 and EDNRBDelta2 share the same transcription initiation site and are 560bp upstream of the conventional hEDNRB, whereas that of EDNRBDelta3 is 939bp upstream from that described for the conventional hEDNRB. Interestingly, many transcription factor motifs are detectable in the upstream regions of these transcription initiation sites. The predicted amino acid sequences reveal that EDNRBDelta1 and EDNRBDelta2 produce the same protein as the conventional hEDNRB, but EDNRBDelta3 would give rise to additional in-frame 89- or 83-amino-acid residues at the N-terminus. EDNRBDelta3 generates the same amino acid sequence at the C terminus, but utilizes the polyadenylation signal within the open reading frame, resulting in a shorter 3'UTR. These transcripts are widely expressed in human tissues, but their expression patterns vary between different tissues.

3' Untranslated Regions↗
PubMed1992

Molecular identification of the gene responsible for congenital nephrogenic diabetes insipidus.

Antidiuretic hormone (arginine vasopressin) binds to and activates V2 receptors in renal collecting tubule cells. Subsequent stimulation of the Gs/adenylyl cyclase system promotes insertion of water pores into the luminal membrane and thereby reabsorption of fluid. In congenital nephrogenic diabetes insipidus (CNDI), an X-linked recessive disorder, the kidney fails to respond to arginine vasopressin. Here we report that an affected male of a family with CNDI has a deletion in the open reading frame of the V2 receptor gene, causing a frame shift and premature termination of translation in the third intracellular loop of the receptor protein. A normal receptor gene was found in the patient's brother. Both the normal and the mutant allele were detected in his mother. A different mutation, causing a codon change in the third transmembrane domain of the V2 receptor, was found in the open reading frame of an affected male but not in the unaffected brother belonging to another family suffering from CNDI.

Adult↗
PubMed2003

Characterization of two alternative promoters for integrase expression in the clc genomic island of Pseudomonas sp. strain B13.

The clc genomic island is a 105 kb integrative and conjugative element (ICE) in Pseudomonas sp. strain B13, which encodes metabolism of 3-chlorocatechol. The clc island is integrated in a tRNAGly gene, but can excise and form a circular intermediate in which both ends are connected. The integrase gene (intB13) of the clc genomic island is located at the right end, 202 bp from the junction site facing inwards. Fragments upstream of intB13 in the circular form and in the integrated form were fused to a promoterless gfp gene for Green Fluorescent Protein and introduced in monocopy onto the chromosome of strain B13. Quantitative GFP fluorescence measurements in individual cells of the different B13-derivatives revealed that the circular form fragment contained a strong constitutive promoter (Pcirc) driving intB13 expression in all cells. By using primer extension Pcirc could be mapped near the left end of the clc element and Pcirc can therefore only control intB13 expression when left and right ends are connected as in the circular form. Expression from intB13 upstream fragments from the integrated clc element was weaker than that from Pcirc and only occurred in maximally 15% of individual cells in a culture. A promoter (Pint) could be roughly mapped in this region by using reverse-transcription PCR and by successively shortening the fragment from the 5' end. Transposon mutants in cloned left end sequences of the clc element were selected which had lost the activation potential on the Pint promoter and those which resulted in overexpression of GFP from Pint. The DNA sequence of the region of the transposon insertions pointed to a relatively well conserved area among various other genomic islands. The activator mutants mapped in an open reading frame (ORF) encoding a 175 amino acid protein without any significant similarity to functionally characterized proteins in the databases.

Base Sequence↗
PubMed1999

Molecular characterization of rabE, a developmentally regulated Dictyostelium homolog of mammalian rab GTPases.

The superfamily of small GTPases includes a subgroup, rab proteins, thought to function in the regulation of discrete steps of membrane traffic. Using a screen based on the polymerase chain reaction, we identified six partial gene sequences of novel rab genes from the soil slime mold amoeba, Dictyostelium. Stretches of conserved sequence for these genes identified them clearly as rab GTPases; unique sequences showed these were novel rab genes. A full-length clone for one gene, which we named rabE, was characterized in detail. The coding sequence of rabE was 1.1 kb in length and contained three introns. RNAse protection analysis revealed rabE expression to be under developmental regulation, with an onset of message expression after 8 h of development. Comparison of the rabE amino acid sequence with the database showed that its unique domains were most similar to the products of four mammalian rab genes. Interestingly, only the rabE protein and its four mammalian homologs contained the sequence WDIAGQE, a variation of a conserved GTPase domain. The WDIAGQE motif thus defines a subgroup of rab proteins. Identification of a Dictyostelium homolog of this group of proteins opens an experimental system to explore the structure and function of this group of WDIAGQE-containing rab proteins.

Amino Acid Sequence↗
PubMed1993

Immediate-early transcription over covalently joined genome ends of bovine herpesvirus 1: the circ gene.

Herpesvirus genomes are linear molecules in virions. Prior to replication in host cells, they form circular templates by unknown mechanisms. Examining lytic infection with bovine herpesvirus 1, we observed immediate-early transcription over joined genome ends, which suggested that circles are present at the initial stage of infection. Among the transcripts was a spliced immediate-early RNA (1.5 kb) sharing exon 1 with previously described major immediate-early transcripts from the right genome end and exon 2 with a late transcript located near the left genome end. Exon 2 encodes a putative circ-encoded protein with homology to the varicella-zoster virus open reading frame 2 and equine herpesvirus 1 open reading frame 3 products. The novel features reported here for bovine herpesvirus 1 may constitute a more general property of herpesviruses.

Amino Acid Sequence↗
PubMed1997

Alternative expression of platelet glycoprotein Ib(beta) mRNA from an adjacent 5' gene with an imperfect polyadenylation signal sequence.

Glycoprotein (GP) Ib is a major component of the platelet membrane receptor for von Willebrand factor, designated the GP Ib-IX-V complex. GP Ib is composed of two subunits (GP Ib(alpha) and GP Ib(beta)) each synthesized from separate genes. The 206 amino acid precursor of GP Ib(beta) is synthesized from a 1.0-kb mRNA expressed by megakaryocytes and was originally characterized from cDNA clones of human erythroleukemic (HEL) cell mRNA, a cell line exhibiting megakaryocytic-like properties. The cell line CHRF-288-11 also exhibits megakaryocytic-like properties, but synthesizes two related GP Ib(beta) mRNA species of 3.5 and 1.0 kb. We performed cDNA cloning experiments to identify the origin of the 3.5-kb transcript and determine its relationship to the 1.0-kb GP Ib(beta) mRNA found in megakaryocytes, platelets, and HEL cells. Our cloning experiments demonstrate that the longer transcript results from a nonconsensus polyadenylation recognition sequence, 5'AACAAT3', within a separate gene located upstream to the platelet GP Ib(beta) gene. In the absence of normal polyadenylation the more 5' gene uses the polyadenylation site within its 3' neighbor, the platelet GP Ib(beta) gene. This newly identified 5' gene contains an open reading frame encoding 369 amino acids with a high degree of sequence similarity to an expanding family of GTP-binding proteins.

Amino Acid Sequence↗
PubMed1992

Mls: a link between immunology and retrovirology.

The nature of the mysterious minor lymphocyte stimulating (Mls) antigens has recently been clarified. These molecules which were key elements for our current understanding of immune tolerance, have a strong influence on the mouse immune system and are encoded by the open reading frame (orf) of endogenous and exogenous mouse mammary tumor viruses (MMTV's). The knowledge that these antigens are encoded by cancerogenic retroviruses opens an interdisciplinary approach for understanding the mechanisms of immune responses and immune tolerance, retroviral carcinogenesis, and retroviral strategies for infection.

Amino Acid Sequence↗
PubMed1998

Type 2 rice metallothionein-like gene has two introns.

A type 2 rice metallothionein-like gene was isolated from root by PCR and sequenced. The PCR fragment was designated as pcr1460, which overlaps with OsMT-2, a cDNA sequence previously characterized, with the presence of two additional segments, 583 and 613 bp in length. These segments are recognized as introns which divide the coding sequence into three exons, 65, 78 and 106 base pairs in length. The sequences flanking the introns conform with the GT/AG rule for splice junctions, and one exonic open reading frame can be identified in each of the introns. The observation that MT-like gene has two introns is the first of such a finding obtained from monocotyledonous plants.

Amino Acid Sequence↗
PubMed1988

Cloning and sequencing of Pseudomonas genes encoding vanillate demethylase.

A 2,598-base-pair (bp) SalI-HincII DNA fragment has been cloned which codes for vanillate demethylase, the enzyme responsible for the demethylation of vanillate (3-methoxy-4-hydroxybenzoate) to protocatechuate (3,4-dihydroxybenzoate). Complementation and insertional inactivation experiments have shown that this fragment carries two genes (vanA and vanB) which are predominantly cotranscribed from a promoter upstream of vanA. Nucleotide sequencing of the SalI-HincII fragment confirmed the genetic data: two open reading frames of 987 and 942 bp were present in the transcribed orientation. These had a very high G + C content in the third base of each codon, which is characteristic of Pseudomonas chromosomal genes. Expression of the genes in Escherichia coli with the T7 RNA polymerase-promoter system gave rise to two polypeptides of 36 and 33 kilodaltons which could be identified by deletion analysis as the products of vanA and vanB, respectively. A search of the protein sequence data bank indicated that the vanB gene product was related to the ferredoxin family.

Amino Acid Sequence↗
PubMed1994

Nucleotide sequence analysis of a 38.5-kilobase-pair region of the genome of human herpesvirus 6 encoding human cytomegalovirus immediate-early gene homologs and transactivating functions.

Human herpesvirus 6 (HHV-6) is prevalent in the human population, with primary infection occurring early in life. Its predominant CD4+ T-lymphocyte tropism, its ability to activate human immunodeficiency virus type 1 (HIV-1) gene expression in vitro, and its upregulation of CD4 expression has led to speculation that HHV-6 may act as a positive cofactor in the progression of HIV infection to AIDS in individuals infected with both viruses. Previous sequencing studies of restricted regions of the 161.5-kbp genome of HHV-6 have demonstrated unequivocally that it is a member of the betaherpesvirus subgroup and have indicated that the HHV-6 genome is generally collinear with the unique long (UL) component of human cytomegalovirus (HCMV). In the work described in this report we have extended these sequencing studies by determining the primary structure of 38.5-kbp of the HHV-6 genome (genomic position 21.0 to 59.5 kbp). Within the sequenced region lie 31 open reading frames, 20 of which are homologous to positional counterparts in HCMV. Of particular significance is the identification of homologs of the HCMV UL36-38 and US22-type genes, which have been shown to encode transactivating proteins. We show that DNA sequences encoding these HHV-6 homologs were able to transactivate HIV-1 long terminal repeat-directed chloramphenicol acetyltransferase expression in cotransfection assays, thus demonstrating functional as well as structural conservation of these betaherpesvirus-specific gene products. Our data therefore confirm the close relationship between HHV-6 and HCMV and identify putative immediate-early regulatory genes of HHV-6 likely to play key roles in lytic replication and possibly also in the interactions between HHV-6 and HIV in dually infected cells.

Animals↗
PubMed1998

Ilarviruses encode a Cucumovirus-like 2b gene that is absent in other genera within the Bromoviridae.

We found that RNA 2 of the four ilarviruses sequenced to date encodes an additional conserved open reading frame (ORF), 2b, that overlaps the 3' end of the previously known ORF, 2a. A novel RNA species of 851 nucleotides was found to accumulate to high levels in plants infected with spinach latent virus (SpLV). Further analysis showed that RNA 4A is a subgenomic RNA of RNA 2 and encodes all of ORF 2b. Moreover, a protein species of the size expected for SpLV ORF 2b was translated in vitro from the RNA 4A-containing virion RNAs. The data support the suggestion that the SpLV 2b protein is translated in vivo. The 2b gene of ilarviruses, which is not encoded by alfamoviruses and bromoviruses, shares several features with the previously reported cucumovirus 2b gene; however, their encoded proteins share no detectable sequence similarities. The evolutionary origin of the 2b gene is discussed.

Amino Acid Sequence↗
PubMed1997

Comparison of a 20 kb region of human herpesvirus 6B with other human beta herpesviruses reveals conserved replication genes and adjacent divergent open reading frames.

The sequence of a 20.15 kb region from human herpesvirus 6 variant B (HHV-6B) strain Z29 is described (GenBank accession number L14772). Determinations of protein homologies for seventeen predicted gene products revealed HHV-6B homologs of six proteins well-conserved both in genetic context and amino acid sequence throughout the alpha-, beta-, and gammaherpesvirus subfamilies. These include proteins involved in viral DNA replication, packaging and nucleotide metabolism, and conserved proteins of undefined function. The close evolutionary relationship of the human betaherpesviruses, HHV-6B, HHV-6A, HHV-7 and human cytomegalovirus (HCMV) was confirmed by identification of several protein sequences encoded only by these viruses, including homologs of the HCMV early phosphoprotein family and a series of HCMV open reading frames predicted to encode glycoprotein exons. Homologs of essential HSV-1 replication proteins, UL8 and UL9, were also identified. Downstream from the conserved replication locus, each betaherpesvirus contains a region of divergent, small open reading frames. The evolution of this region and its potential use in the development of a viral vector system are discussed.

Conserved Sequence↗
PubMed1993

The VP35 and VP40 proteins of filoviruses. Homology between Marburg and Ebola viruses.

The fragments of genomic RNA sequences of Marburg (MBG) and Ebola (EBO) viruses are reported. These fragments were found to encode the VP35 and VP40 proteins. The canonic sequences were revealed before and after each open reading frame. It is suggested that these sequences are mRNA extremities and at the same time the regulatory elements for mRNA transcription. Homology between the MBG and EBO proteins was discovered.

Amino Acid Sequence↗
PubMed1995

The sequence of the rat pyruvate carboxylase-encoding cDNA.

A composite 3945-bp cDNA that encodes rat pyruvate carboxylase (PC) has been constructed from clones isolated from a rat liver cell cDNA library and the nucleotide sequence has been determined. The rat cDNAs open reading frame encodes a protein of 1178 amino acids that is 98.6% identical (99.0% similar) to that of mouse PC and 96.0% identical (97.8% similar) to that of human PC.

Amino Acid Sequence↗
PubMed1998

A method for the identification of promoters recognized by RNA polymerase containing a particular sigma factor: cloning of a developmentally regulated promoter and corresponding gene directed by the Streptomyces aureofaciens sigma factor RpoZ.

We have developed a method for the identification of promoters recognized by a particular sigma factor of RNA polymerase, based on a two-compatible plasmid system in Escherichia coli (Ec). Using the method, a DNA fragment containing the promoter, PREN40, recognized by sporulation-specific Streptomyces aureofaciens (Sa) sigma factor RpoZ, was cloned. High-resolution S1 nuclease mapping using RNA prepared from Ec, and Sa from various developmental stages has shown a high degree of similarity of PREN40 to consensus sequence of flagellar and chemotaxis promoters. The promoter was induced at the time of aerial mycelium formation, and was off in the Sa strain with the rpoZ-disrupted gene. A promoter-bearing DNA fragment was inserted into the promoter-probe plasmid pARC1 to give expression patterns consistent with the results of direct RNA analysis. The region downstream of the promoter was cloned in Sa. Sequence analysis revealed an open reading frame (ORF) of 283 amino acids (Mr 30006), encoding a highly basic (pI 12.35) protein with high percentage of serine, threonine and alanine (41.8%).

Alanine↗