Intronless Open Reading Frame Research Articles

Discovery of Three Novel G-Protein-Coupled Receptor Genes

We report here the molecular cloning, tissue distribution, and chromosomal localization of novel genes encoding G-protein-coupled receptors (GPCRs). A search of a mouse database of expressed sequence tags revealed an EST partially encoding a GPCR, which was used to screen a mouse genomic library to obtain the translational open reading frame (ORF). The resultant clone, GPR27, contained an intronless ORF, encoding a receptor of 379 amino acids. In an alternate strategy, human genomic DNA was subjected to polymerase chain reaction (PCR) amplification, using degenerate oligonucleotides based on GPR1. Two PCR products partially encoding GPCRs were isolated and used to screen a genomic library to obtain the translational ORF. One of the resultant clones, GPR30, contained an intronless ORF encoding a receptor of 375 amino acids. The other clone, GPR35, also contained an intronless ORF encoding a receptor of 309 amino acids. Transcripts corresponding to GPR27 and GPR30 were detected in several areas of human and rat CNS, while GPR35 expression was detected only in the rat intestine. Through fluorescencein situhybridization analysis the gene encoding GPR30 was localized to chromosome 7p22 and GPR35 to chromosome 2q37.3.

Molecular Cloning of the Dog β1 and β2 Adrenergic Receptors

We report the isolation of the genes encoding the β1 and β2 adrenergic receptors from dog genomic DNA. Sequence analysis of both genes revealed intronless open reading frames of 473 and 415 amino acid residues, receptively. Heterologous expression of both receptors in CHO cells indicated that both receptors are functionally similar to the human homologs. Comparing the dog β1 and β2 adrenergic receptors, the β1 receptor appears to bind to G proteins more tightly than the β2 receptor. Heterologously expressed receptors provide a convenient system for evaluating novel receptor agonists and antagonists.

Structural and Functional Characterization of Human Potassium Channel Subunit β1 (KCNA1B)

Voltage-activated Shaker-related potassium channels (Kv1) consist of α and β subunits. We have analysed the structure of the human KCNA1B (hKvβ1) gene. KCNA1B is >250 kb in size and encodes at least three Kvβ1 splice variants. The Kvβ1 open reading frame is divided into 14 exons. In contrast, genes coding for family members of KCNA (Kv1α) subunits are markedly smaller and have intronless open reading frames. The expression of Kv1α and Kvβ mRNA was compared in Northern blots of poly(A+) RNA isolated from various human brain tissues. The results suggest an intricate and cell-specific regulation of Kv1α and Kvβ mRNA synthesis such that distinct combinations of α and β subunits would occur in different nuclei of the brain. The splice variants hKvβ1.1 and hKvβ1.2 were functionally characterized in coexpression studies with hKv1.5α subunits in 293 cells. It is shown that they confer rapid inactivation on hKv1.5 channels with different potencies. This may be due to differences in their amino terminal sequences and/or inactivating domains. It is also shown that the amino terminal Kvβ1.1 and Kv1.4α inactivating domains compete with each other, probably for the binding to the same receptor site(s) on Kv1α-subunits. Copyright @ 1996 Elsevier Science Ltd

Mutation avoidance and DNA repair proficiency in Ustilago maydis are differentially lost with progressive truncation of the REC1 gene product.

The REC1 gene of Ustilago maydis has an uninterrupted open reading frame, predicted from the genomic sequence to encode a protein of 522 amino acid residues. Nevertheless, an intron is present, and functional activity of the gene in mitotic cells requires an RNA processing event to remove the intron. This results in a change in reading frame and production of a protein of 463 amino acid residues. The 3'-->5' exonuclease activity of proteins derived from the REC1 genomic open reading frame, the intronless open reading frame, and several mutants was investigated. The mutants included a series of deletions constructed by removing restriction fragments at the 3' end of the cloned REC1 gene and a set of mutant alleles previously isolated in screens for radiation sensitivity. All of these proteins were overproduced in Escherichia coli as N-terminal polyhistidine-tagged fusions that were subsequently purified by immobilized metal affinity chromatography and assayed for 3'-->5' exonuclease activity. The results indicated that elimination of the C-terminal third of the protein did not result in a serious reduction in 3'-->5' exonuclease activity, but deletion into the midsection caused a severe loss of activity. The biological activity of the rec1-1 allele, which encodes a truncated polypeptide with full 3'-->5' exonuclease activity, and the rec1-5 allele, which encodes a more severely truncated polypeptide with no exonuclease activity, was investigated. The two mutants were equally sensitive to the lethal effect of UV light, but the spontaneous mutation rate was elevated 10-fold over the wild-type rate in the rec1-1 mutant and 100-fold in the rec1-5 mutant. The elevated spontaneous mutation rate correlated with the ablation of exonuclease activity, but the radiation sensitivity did not. These results indicate that the C-terminal portion of the Rec1 protein is not essential for exonuclease activity but is crucial in the role of REC1 in DNA damage repair.

Cloning, sequencing, and expression of the rhesus monkey beta 2 adrenergic receptor.

The beta 2 adrenergic receptor (beta 2AR) plays a key role in the signal transduction mechanism for epinephrine and norepinephrine. The gene for beta 2 adrenergic receptors has been cloned for several species, but has remained undetermined for rhesus monkey. In this study, we report the isolation of the gene encoding the rhesus beta 2AR from both cDNA and genomic DNA sources. Sequence analysis of the gene reveals an intronless open reading frame that encodes a 415-amino-acid protein. The rhesus receptor is highly homologous to that from other species, especially to the human receptor (97% sequence identity). Functional characterization by ligand binding and agonist-mediated cAMP accumulation indicates that the rhesus beta 2 receptor shares a very similar pharmacological profile with the human beta 2 receptor. Therefore, the rhesus monkey represents a valid animal model for developing therapeutic agents targeted at the corresponding human beta 2 receptor.

Urbs1, a gene regulating siderophore biosynthesis in Ustilago maydis, encodes a protein similar to the erythroid transcription factor GATA-1.

Ustilago maydis secretes ferrichrome-type siderophores, ferric-ion-binding compounds, in response to iron starvation. TA2701, a non-enterobactin-producing, non-ferrichrome-utilizing mutant of Salmonella typhimurium LT-2, was employed as a biological indicator in a novel screening method to isolate three N-methyl-N'-nitro-N-nitrosoguanidine-induced U. maydis mutants defective in the regulation of ferrichrome-type siderophore biosynthesis. These mutants displayed a constitutive phenotype; they produced siderophores in the presence of iron concentrations that would typically repress siderophore synthesis in wild-type strains. A 4.8-kb fragment of U. maydis genomic DNA capable of restoring normal regulation of siderophore biosynthesis in the constitutive mutants was identified. This segment of DNA contains an intronless open reading frame that specifies a protein of 950 amino acids containing two finger motifs similar to those found in the erythroid transcription factor GATA-1. Disruption of this open reading frame in a wild-type strain gave rise to cells that produced siderophores constitutively. Genetic studies indicated that the disruption mutation was allelic to the chemically induced mutations, confirming that the structural gene for a regulator rather than a suppressor gene had been cloned. Northern (RNA) analysis of the gene revealed a 4.2-kb transcript that is expressed constitutively at low levels in wild-type cells. The data support the hypothesis that this gene, which we designate urbs1 (Ustilago regulator of biosynthesis of siderophores), acts directly or indirectly to repress biosynthesis of siderophores in U. maydis.

Urbsl, a Gene Regulating Siderophore Biosynthesis in Ustilago maydis, Encodes a Protein Similar to the Erythroid Transcription Factor GATA-1

Ustilago maydis secretes ferrichrome-type siderophores, ferric-ion-binding compounds, in response to iron starvation. TA2701, a non-enterobactin-producing, non-ferrichrome-utilizing mutant of Salmonella typhimurium LT-2, was employed as a biological indicator in a novel screening method to isolate three N-methyl-N'-nitro-N-nitrosoguanidine-induced U. maydis mutants defective in the regulation of ferrichrome-type siderophore biosynthesis. These mutants displayed a constitutive phenotype; they produced siderophores in the presence of iron concentrations that would typically repress siderophore synthesis in wild-type strains. A 4.8-kb fragment of U. maydis genomic DNA capable of restoring normal regulation of siderophore biosynthesis in the constitutive mutants was identified. This segment of DNA contains an intronless open reading frame that specifies a protein of 950 amino acids containing two finger motifs similar to those found in the erythroid transcription factor GATA-1. Disruption of this open reading frame in a wild-type strain gave rise to cells that produced siderophores constitutively. Genetic studies indicated that the disruption mutation was allelic to the chemically induced mutations, confirming that the structural gene for a regulator rather than a suppressor gene had been cloned. Northern (RNA) analysis of the gene revealed a 4.2-kb transcript that is expressed constitutively at low levels in wild-type cells. The data support the hypothesis that this gene, which we designate urbs1 (Ustilago regulator of biosynthesis of siderophores), acts directly or indirectly to repress biosynthesis of siderophores in U. maydis.

Molecular cloning and functional expression of 5-HT1E-like rat and human 5-hydroxytryptamine receptor genes.

Sequential polymerase chain reaction experiments were performed to amplify a unique sequence representing a guanine nucleotide-binding protein (G-protein)-coupled receptor from rat hypothalamic cDNA. Degenerate oligonucleotides corresponding to conserved amino acids from transmembrane domains III, V, and VI of known receptors [5-HT1A, 5-HT1C, and 5-HT2; 5-HT is serotonin (5-hydroxytryptamine)] were used as primers for the sequential reactions. The resulting product was subcloned and used to screen a rat genomic library to identify a full-length clone (MR77) containing an intronless open reading frame encoding a 366-amino acid seven-transmembrane domain protein. The human homolog was isolated, and its encoded protein had 93% overall amino acid identity with the rat sequence. Within the conserved transmembrane domains, the sequences exhibit approximately 52%, 59%, 65%, and 68% amino acid identity with the known rat 5-HT1A, rat 5-HT1B, rat 5-HT1D, and human 5-HT1E receptors, respectively. MR77 was subcloned into a eukaryotic expression vector system and expressed in CosM6 cells. Studies on broken cell preparations indicate that the expressed receptor exhibits 125I-labeled d-lysergic acid diethylamide (LSD) binding that can be displaced by serotonin but not by other biogenic amines. The specific binding is displaced by the selective 5-HT1D agonist sumatriptan but not by the mixed 5-HT1A/1D agonist 5-carboxyamidotryptamine. 125I-labeled LSD binding was competitively antagonized by the ergot alkaloids methysergide and ergotamine. HeLa cells transfected with the MR77 gene exhibited inhibition of adenylate cyclase in response to serotonin. MR77 is expressed at low levels throughout the brain, with the greatest expression in the cortex, hippocampus, and striatum. MR77 thus represents a 5-HT receptor of the 5-HT1 class, and we propose that, based on the pharmacological characterization, MR77 represents an additional 5-HT1E-like receptor.

Cloning and expression of the human 5-HT1B-type receptor gene

We report the cloning and expression of a novel 5-HT receptor gene from human genomic DNA. This clone, HGCR1, contains an apparently intronless open reading frame of 390 amino acids with the seven hydrophobic regions, typical of G-protein coupled receptors. The deduced amino acid sequence of HGCR1 is 39%, 55% and 87% identical to that for the human 5-HT 1A, the human 5-HT 1D and the rat 5-HT 1B receptor, respectively. [ 3H]5-HT binding to transfected COS-7 cell membranes yields a pharmacological profile similar to that of 5-HT 1B receptor. Thus these findings indicate the presence of 5-HT 1B-type receptor in the human.

CENP-B is a highly conserved mammalian centromere protein with homology to the helix-loop-helix family of proteins

CENP-B is a centromere associated protein originally identified in human cells as an 80 kDa autoantigen recognized by sera from patients with anti-centromere antibodies (ACA). Recent evidence indicates that CENP-B interacts with centromeric heterochromatin in human chromosomes and may bind to a specific subset of human alphoid satellite DNA. CENP-B has not been unambiguously identified in non-primates and could, in principal, be a primate-specific alphoid DNA binding protein. In this work, a human genomic DNA segment containing the CENP-B gene was isolated and subjected to DNA sequence analysis. In vitro expression identified the site for translation initiation of CENP-B, demonstrating that it is encoded by an intronless open reading frame (ORF) in human DNA. A homologous mouse gene was also isolated and characterized. It was found to possess a high degree of homology with the human gene, containing an intronless ORF coding for a 599 residue polypeptide with 96% sequence similarity to human CENP-B. 5' and 3' flanking and untranslated sequences were conserved at a level of 94.6% and 82.7%, respectively, suggesting that the regulatory properties of CENP-B may be conserved as well. CENP-B mRNA was detected in mouse cells and tissues and an immunoreactive nuclear protein identical in size to human CENP-B was detected in mouse 3T3 cells using human ACA. Analysis of the sequence of CENP-B revealed a segment of significant similarity to a DNA binding motif identified for the helix-loop-helix (HLH) family of DNA binding proteins. These data demonstrate that CENP-B is a highly conserved mammalian protein that may be a member of the HLH protein family and suggest that it plays a role in a conserved aspect of centromere structure or function.

Cloning, functional expression, and mRNA tissue distribution of the rat 5-hydroxytryptamine1A receptor gene.

G protein-coupled receptors comprise a family of genes that share significant sequence similarity. We have screened a rat genomic library under low stringency hybridization conditions with the coding portion of the hamster beta 2-adrenergic receptor gene to isolate new members of this gene family. We show that one of these clones, clone D, codes for a 5-hydroxytryptamine1A (5-HT1A) binding site since: 1) it possesses an intronless open reading frame encoding a protein with seven putative transmembrane domains and 89% amino acid identity with the human 5-HT1A receptor (G21); 2) when transfected into Ltk- cells, it expresses a ligand-binding site with the pharmacology of the 5-HT1A receptor subtype, including 5-HT- and spiroxatrine-displaceable binding of 8-hydroxy-(2-(N,N-di[2,3-3H]propylamino)-1,2,3,4-tetrahydronaphthalene (KH = 0.8 nM). We further show that clone D encodes a functional receptor because its binding site interacts with G proteins and because it mediates agonist-induced inhibition of basal and stimulated cAMP accumulation in transfected GH4C1 pituitary cells. Finally, we have analyzed the tissue distribution of 5-HT1A receptor mRNA in rat brain and have found that 5-HT1A mRNA is present with the expected distribution of the 5-HT1A receptor (highest in septum and hippocampus) but is present as three RNA species (3.9, 3.6, and 3.3 kilobases). These studies represent the first characterization of receptor function and brain distribution of the cloned rat 5-HT1A receptor.

Characterization of the kafirin gene family from sorghum reveals extensive homology with zein from maize

Electrophoretic analysis of translation products of polyadenylated RNA isolated from mid-maturation sorghum seed in the presence of [(35)S]met, [(3)H]leu, or [(3)H]val revealed two major proteins of kDa and 21 kDa. These products were not detected when [(3)H]lys was supplied as the radioactive substrate. Under similar electrophoretic conditions, kafirin (a major seed storage prolamin of sorghum), migrated as two bands of 22 kDa and 19 kDa. Sequence analysis of two cDNA clones (pSK8 and pSKR2) from sorghum seed mRNA revealed them to be highly homologous with each other and to the 22 kDa zeins from maize, suggesting that they represented kafirin cDNAs. Compared with pSKR2, pSK8 had an insertion of 24 nucleotides and a deletion of 24 nucleotides, so that the coding regions were nearly identical in length. The deduced amino acid sequence for these cDNA clones reveals that kafirin, like zein, is rich in glutamine and nonpolar amino acids, but contains no lysine. Both kafirin and zein have a 21 amino acid signal peptide exhibiting 80% homology and eight copies of a repetitive amino acid block in the C-terminal domain with the consensus: infI (supP) LL finP (supA) LN infQ (supP) LALANPAAYLQQQQ.The kafirin cDNAs were used as probes to screen a sorghum genomic library; one genomic clone (λGK.1) was sequenced and found to be very similar (97.8%) to the pSK8 cDNA clone. Clone λGK.1 contains features typical for a functional gene in that the intronless open reading frame encoding 268 amino acids is flanked at the 5' end by sequences corresponding to the CAAT and TATA promoter boxes (positioned at about -60 and -30 bp, respectively, from the transcriptional initiation site), and at the 3' end by a consensus polyadenylation signal. In common with zein genomic clones, kafirin clones contain a 15 basepair consensus sequence centered at postion -320 relative to the transcriptional initiation site. Under similar hybridization conditions, genomic reconstruction analysis using an oligonucleotide probe indicated the presence of less than 20 copies of kafirin per haploid sorghum genome compared with approximatley 140 copies of zein per haploid maize genome.

Homology between the photoreactivation genes of Saccharomyces cerevisiae and Escherichia coli

A cloned fragment of Saccharomyces cerevisiae chromosomal DNA carrying the photoreactivation gene ( PHR) has been sequenced. The fragment contains a 1695-bp intronless open reading frame (ORF) coding for a polypeptide of 564 amino acids (aa). The phr gene of Escherichia coli was also sequenced, and the sequence is in agreement with the published data. The yeast PHR gene has a G + C content of 36.2%, whereas 53.7% was found for the E. coli gene. Despite the difference in G + C content there is a 35% homology between the deduced aa sequences. This homology suggests that both genes have originated from a common ancestral gene.