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PubMed1987

Organization and sequence of the hsd genes of Escherichia coli K-12.

The nucleotide sequence of the hsdR and M genes, together with that for hsdS comprises an 8400 base segment spanning the entire hsd region of Escherichia coli K-12. The three hsd genes are transcribed in the same direction, but from two promoters. hsdR and hsdM are separated by 492 base-pairs, whereas the termination codon of hsdM overlaps the initiation codon of hsdS. pres precedes hsdR, and our data indicate a transcription termination signal in the interval between hsdR and pmod, as expected if transcription of hsdM and S is dependent on pmod. Transcription from pres is not influenced by the products of the hsdM and S genes, and the mechanism whereby restriction is prevented when the hsd region is transferred to a modification-deficient cell remains to be elucidated. A segment of the predicted amino acid sequence of the M polypeptide shares homology with a variety of adenine methylases and may identify part of the active site for methylation of specific adenine residues. The R polypeptide shows homology with a variety of ATPases, and pronounced regions of alpha-helical structure are predicted, one of which is amphipathic.

Amino Acid Sequence↗

PubMed1998

Phylogenetic analysis of the S10 gene of field and laboratory strains of bluetongue virus from the United States.

The sequence of the S10 gene segment of the United States prototype strains of BTV serotypes 10, 11, 13, and 17 obtained from the American Type Culture Collection (ATCC), the commercial modified live virus vaccine strains of BTV serotypes 10, 11, and 17, and 20 field isolates of BTV serotypes 10, 11, 13, and 17 was determined to better define the molecular epidemiology of BTV infection in the US. All S10 gene segments were 822 nucleotides in length with two in-frame initiation codons (nucleotides 20 to 22 and 59 to 61) and a single termination codon (nucleotides 707 to 709), thus all S10 genes were predicted to encode two proteins (NS3, NS3A). Nucleotide differences between the S10 genes from field isolates of BTV ranged from zero (100% identity) to 142 (81.8% identity). The sequences of the S10 gene segments from the US prototype ATCC strains of BTV 10 and 11 were very different from the previously published sequences of putative US prototype viruses of the same serotypes (Lee and Roy, 1986; Hwang et al., 1992). Comparison of the predicted NS3/NS3A proteins encoded by the S10 gene showed little variation between the various viruses (from 93 to 100% identity). This apparent conservation of NS3/NS3A amongst different strains and serotypes of BTV likely is a reflection of functional constraints on the protein that tolerate little variation. The various US isolates of BTV segregate into two distinct monophyletic groups based on their S10 gene sequences and clustering of viruses was independent of serotype, year of isolation, geographical origin, and of host species of isolation. The S10 sequence data also show that viruses that segregated within each of these two monophyletic groups co-circulated in the western US between 1953 and 1990, and that reassortment of the S10 gene segment likely occurs in nature. Comparison of dendograms derived from sequence analysis of the S3 (de Mattos et al., 1996)and the S10 gene segments from the same viruses also indicates that the S10 gene segment evolves and reassorts independently of the S3 gene segment.

Animals↗

PubMed2002

Characterization of the p10 gene region of Anticarsia gemmatalis nucleopolyhedrovirus.

The Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV) p10 gene region was cloned, sequenced and the putative p10 gene expression characterized by Northern-blot analysis. Sequence analysis of the p10 gene region indicated the presence of two complete open reading frames (ORFs) of 713 and 281 nucleotides, which codes for polypeptides of 273 and 93 amino acids, with homology to the P26 and P10 proteins of baculoviruses, respectively. Two additional partial ORFs, coding for partial polypeptides of 110 and 146 amino acids, showed homology to the p22.2 gene of Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) and p74 genes of different baculoviruses, respectively. A small ORF of 224 nucleotides coding for a protein of 74 amino acids showed homology to the 3'-end of the early p94 gene of AcMNPV. A putative baculovirus very late promoter motif TAAG was identified in the 5'-non-translated region (5'-UTR) at position-54 upstream of the start codon. The consensus polyadenylation sequence AATAAA is present 146nt downstream of the termination codon and the p10 ORF is flanked by the p26 and p74 ORFs. Homology comparisons showed that the P10 protein of AgMNPV is most closely related (82% amino acid sequence identity) to the P10 from the Orgyia pseudotsugata nucleopolyhedrovirus (OpMNPV). Transcriptional analysis of the AgMNPV p10 gene showed that p10-specific transcripts could be detected late in infection.

Amino Acid Sequence↗

PubMed2004

The Human hydroxyacylglutathione hydrolase (HAGH) gene encodes both cytosolic and mitochondrial forms of glyoxalase II.

In yeast and higher plants, separate genes encode the cytosolic and mitochondrial forms of glyoxalase II. In contrast, although glyoxalase II activity has been detected both in the cytosol and mitochondria of mammals, only a single gene encoding glyoxalase II has been identified. Previously it was thought that this gene (the hydroxyacylglutathione hydrolase gene), comprised 8 exons that are transcribed into mRNA and that the resulting mRNA species encoded a single cytosolic form of glyoxalase II. Here we show that this gene gives rise to two distinct mRNA species transcribed from 9 and 10 exons, respectively. The 9-exon-derived transcript encodes two protein species: mitochondrially targeted glyoxylase II, which is initiated from an AUG codon in a previously uncharacterized part of the mRNA sequence, and cytosolic glyoxalase II, which is initiated by internal ribosome entry at a downstream AUG codon. The transcript deriving from 10 exons has an in-frame termination codon between the two initiating AUG codons and hence only encodes the cytosolic form of the protein. Confocal fluorescence microscopy indicates that the mitochondrially targeted form of glyoxalase II is directed to the mitochondrial matrix. Analysis of glyoxalase II mRNA sequences from a number of species indicates that dual initiation from alternative AUG codons is conserved throughout vertebrates.

Alternative Splicing↗

PubMed2000

Molecular alterations involving p53 codons 167 and 183 in papillary thyroid carcinomas from chernobyl-contaminated regions of belarus.

After the Chernobyl accident in 1986, there was a significant increase in the incidence of papillary thyroid carcinoma in fallout-exposed children from Belarus. We studied the p53 gene from 24 papillary thyroid carcinoma cases presenting in 1996. All subjects lived in contaminated regions of Belarus at the time of the accident and were under age 20 when exposed to fallout. Exons 5 through 9 of p53 were amplified from genomic tumor DNA using the polymerase chain reaction (PCR). The PCR products were analyzed by direct DNA sequencing using an automated sequencer. Five cases each exhibited two molecular alterations within exon 5. Alterations were confirmed by sequencing in both directions. One alteration, involving codon 167 (CAG-->CAT) in all five cases, resulted in the substitution of HIS for GLN. The second alteration, involving codon 183 (TCA-->TGA) in all five cases, resulted in a premature termination codon. Leukocyte DNA from each of the positive cases was analyzed and found to contain only wild-type p53 sequence. These results suggest that mutations involving codons 167 and 183 in the p53 locus are important in the pathogenesis of a subset (21%) of radiation-induced papillary thyroid carcinomas from Belarus.

Adolescent↗

PubMed1994

Molecular cloning and sequence analysis of the proBA operon from an extremely thermophilic eubacterium Thermus thermophilus.

A 3.6 kb DNA fragment carrying the Thermus thermophilus proBA region, which encodes the first two steps in the proline biosynthetic pathway, was cloned from the Thermus thermophilus gene library, and its complete nucleotide sequence was determined. The deduced amino acid sequence of gamma-glutamyl kinase (40,657 Da), the product of proB gene, and gamma-glutamyl phosphate reductase (48,747 Da), the product of proA gene, showed 44.1% and 44.4% identity to those of Escherichia coli, respectively. The termination codon of the proB gene and the initiation codon of the proA gene overlapped by 2 bp. A possible transcriptional termination structure was found downstream of the proA gene but not downstream of the proB gene. These results indicate that the proBA genes of T. thermophilus form a single operon as in E. coli.

Aldehyde Oxidoreductases↗

PubMed1989

DNA sequence analysis, gene product identification, and localization of flagellar motor components of Escherichia coli.

The Escherichia coli operon designated flaA contains seven flagellar genes; among them are two switch protein genes whose products are believed to interface with the motility and chemotaxis machinery of the cell. Complementation analysis using several plasmids carrying different portions of the flaA operon and analysis of expression of these plasmids in minicells allowed the identification of two flagellar gene products. The MotD (now called FliN) protein, a flagellar switch protein, was determined to have an apparent molecular weight of 16,000, and the FlaAI (FliL) protein, encoded by a previously unidentified gene, had an apparent molecular weight of 17,000. DNA sequence analysis of the motD gene revealed an open reading frame of 414 base pairs. There were two possible initiation codons (ATG) for motD translation, the first of which overlapped with the termination codon of the upstream gene, flaAII (fliN). The wild-type flaAI gene on the chromosome was replaced with a flaAI gene mutated in vitro. Loss of the flaAI gene product resulted in a nonmotile and nonflagellated phenotype. The subcellular location for both the MotD and FlaAI proteins was determined; the FlaAI protein partitioned exclusively in the insoluble fraction of a whole minicell sonic extract, whereas the MotD protein remained in both the soluble and insoluble fractions. In addition, we subcloned a 2.2-kilobase-pair DNA fragment capable of complementing the remaining four genes of the flaA operon (flbD [fliO], flaR [fliP], flaQ [fliQ], and flaP [fliR]).

Amino Acid Sequence↗

PubMed1984

Murine leukemia virus mutant with a frameshift in the reverse transcriptase coding region: implications for pol gene structure.

The molecular defect in the nonconditional B-tropic MuLV pol mutant, clone 23 (Gerwin et al., J. Virol. 31:741-751, 1979), has been characterized by recombinant DNA technology. The entire mutant genome was cloned from an EcoRI digest of integrated cellular DNA into bacteriophage lambda Charon 4A and then subcloned at the EcoRI site of pBR322. NIH-3T3 cells transfected with the plasmid clone, termed pRTM (RTM, reverse transcriptase mutant), reproduced the properties of clone 23 virus-infected cells. In vivo ligation experiments involving cotransfection of subclones of pRTM and wild-type murine leukemia virus localized the defect in the clone 23 genome to an approximately 400-base-pair region in the pol gene between the SalI and XhoI sites. Sequence analysis of this region in the wild-type and mutant genomes revealed that the mutant has one additional C residue located 231 bases downstream of the last base of the SalI recognition site. This 1-base insertion brings three TGA termination codons into phase. Thus, the mutation in clone 23 leads to premature termination of translation, explaining the presence in clone 23 virions of a truncated polymerase with low levels of enzymatic activity. It was previously shown that the gag precursor is cleaved normally in clone 23-infected cells; therefore, if a virus-coded protease is involved in this cleavage, it must be encoded by sequences upstream of the reverse transcriptase region of the pol gene. This consideration, coupled with the observed molecular weight of the mutant polymerase and our precise determination of its C terminus, have led to a proposal for the genetic organization of the murine leukemia virus pol gene.

Animals↗

PubMed2003

Genomic organization of ATOX1, a human copper chaperone.

BACKGROUND: Copper is an essential trace element that plays a critical role in the survival of all living organisms. Menkes disease and occipital horn syndrome (OHS) are allelic disorders of copper transport caused by defects in a X-linked gene (ATP7A) that encodes a P-type ATPase that transports copper across cellular membranes, including the trans-Golgi network. Genetic studies in yeast recently revealed a new family of cytoplasmic proteins called copper chaperones which bind copper ions and deliver them to specific cellular pathways. Biochemical studies of the human homolog of one copper chaperone, ATOX1, indicate direct interaction with the Menkes/OHS protein. Although no disease-associated mutations have been reported in ATOX1, mice with disruption of the ATOX1 locus demonstrate perinatal mortality similar to that observed in the brindled mice (Mobr), a mouse model of Menkes disease. The cDNA sequence for ATOX1 is known, and the genomic organization has not been reported. RESULTS: We determined the genomic structure of ATOX1. The gene contains 4 exons spanning a genomic distance of approximately 16 kb. The translation start codon is located in the 3' end of exon 1 and the termination codon in exon 3. We developed a PCR-based assay to amplify the coding regions and splice junctions from genomic DNA. We screened for ATOX1 mutations in two patients with classical Menkes disease phenotypes and one individual with occipital horn syndrome who had no alterations detected in ATP7A, as well as an adult female with chronic anemia, low serum copper and evidence of mild dopamine-beta-hydroxylase deficiency and no alterations in the ATOX1 coding or splice junction sequences were found. CONCLUSIONS: In this study, we characterized the genomic structure of the human copper chaperone ATOX1 to facilitate screening of this gene from genomic DNA in patients whose clinical or biochemical phenotypes suggest impaired copper transport.

Cation Transport Proteins↗

PubMed1992

Retinoic acid-resistant HL-60R cells harbor a point mutation in the retinoic acid receptor ligand-binding domain that confers dominant negative activity.

Retinoic acid (RA) induces granulocytic differentiation of acute promyelocytic leukemia (APL) cells and is a useful therapeutic agent for patients with this disease. In the HL-60 promyelocytic leukemia cell line, this RA-induced granulocytic differentiation appears to be directly mediated through the RA receptor (RAR-alpha). We have previously identified a mutant subclone of HL-60 (designated HL-60R) that exhibits relative resistance to RA and that harbors RA receptors with markedly reduced affinity for RA. In the present study, we have now identified the genetic basis for this aberrant RA receptor activity. DNA sequencing of polymerase chain reaction-amplified cDNA products corresponding to the RAR-alpha ligand-binding domain shows a point mutation in RAR-alpha codon 411 in this mutant HL-60R subclone. This specific C-->T mutation generates a termination codon resulting in the truncation of 52 amino acids at the COOH terminal end of RAR-alpha. In cotransfection studies, expression vectors harboring this mutated RAR-alpha exhibit dominant negative activity with respect to the trans-activating function of the normal RAR-alpha. Although our observations are limited to HL-60 cells, similar RA receptor mutations might play an important role in the acquisition of RA resistance in RA-treated APL patients.

Amino Acid Sequence↗

PubMed2003

[Genetic diversity analysis of the S10 gene of field and vaccine strains of Bluetongue virus].

S10 gene sequences of 1 attenuated vaccine strain and 31 Chinese field isolates & 1 South Africa strain of BTV were determined. The results revealed that all 33 S10 gene segments have 822 nucleotides in length with two in-frame initiation codons (nucleotides 20 to 22 and 59 to 61) and a common termination codon (nucleotides 707 to 709), which encodes two proteins (NS3 and NS3A). Nucleotide difference in the sequence of all S10 gene were from zero to 107 bp (86.4% - 100% identity). NS3/NS3A protein showed a light difference from zero to 10 amino acid (95.6% - 100% identity). Phylogenetic analysis of the S10 gene of above strains sequenced and 9 other strains from GenBank, segregated the Chinese viruses into a monophyletic group distinct from US viruses; Nucleotide identity was 85% between China Group and US group. The various Chinese isolates segregated into two phyletic subgroups based on S10 gene sequences. The clustering of viruses was dependent of geographical origin, and independent of host species of isolation, serotype & year of isolation.

Animals↗

PubMed1996

The primary structures of the Archaeon Halobacterium salinarium blue light receptor sensory rhodopsin II and its transducer, a methyl-accepting protein.

Recently, a large family of transducer proteins in the Archaeon Halobacterium salinarium was identified. On the basis of the comparison of the predicted structural domains of these transducers, three distinct subfamilies of transducers were proposed. Here we report isolation, complete gene sequences, and analysis of the encoded primary structures of transducer gene htrII, a member of family B, and its blue light receptor gene (sopII) of sensory rhodopsin II (SRII). The start codon ATG of the 714-bp sopII gene is one nucleotide beyond the termination codon TGA of the 2298-bp htrII gene. The deduced protein sequence of HtrII predicts a eubacterial chemotaxis transducer type with two hydrophobic membrane-spanning segments connecting sizable domains in the periplasm and cytoplasm. HtrII has a common feature with HtrI, the sensory rhodopsin I transducer; like HtrI, HtrII possesses a hydrophilic loop structure just after the second transmembrane segment. The C-terminal 299 residues (765 amino acid residues total) of HtrII show strong homology to the signaling and methylation domain of eubacterial transducer Tsr. The hydropathy plot of the primary structure of SRII indicates seven membrane-spanning alpha-helical segments, a characteristic feature of retinylidene proteins ("rhodopsins") from a widespread family of photoactive pigments. SRII shows high identity with SRI (42%), bacteriorhodopsin (BR) (32%), and halorhodopsin (24%). The crucial positions for retinal binding sites in these proteins are nearly identical, with the exception of Met-118 (numbering according to the mature BR sequence), which is replaced by Val in SRII. In BR, residues Asp-85 and Asp-96 are crucial in proton pumping. In SRII, the position corresponding to Asp-85 in BR is conserved, but the corresponding position of Asp-96 is replaced by an aromatic Tyr. Coexpression of the htrII and sopII genes restores SRII phototaxis to a mutant (Pho81) that contains a deletion in the htrI/sopI and insertion in htrII/sopII regions. This paper describes the first example that both HtrI and HtrII exist in the same halobacterial cell, confirming that different sensory rhodopsins SRI and SRII in the same organism have their own distinct transducers.

Amino Acid Sequence↗

PubMed1990

Initiation of translation at a UAG stop codon in the aldolase gene of Plasmodium falciparum.

The gene coding for the key glycolytic enzyme fructose-1,6-diphosphate aldolase of the human malaria parasite Plasmodium falciparum lacks a functional AUG initiation codon for translation. Protein sequences of natural or in vitro translated aldolase include the candidate start methionine residue at internal positions. No additional AUG start codon is found in genomic DNA, cDNA or mRNA sequences. Instead, a UAG chain termination codon is recognized as the start signal of protein synthesis in vivo and in vitro.

Amino Acid Sequence↗

PubMed1990

Suppression and the code: beyond codons and anticodons.

Specificity and accuracy in the decoding of genetic information during mRNA-programmed, ribosome-dependent polypeptide synthesis (translation) involves more than just hydrogen bonding between two anti-parallel trinucleotides, the mRNA codon and the tRNA anticodon. Other macromolecules are also involved, and translational suppression has been and continues to be an appropriate and effective way to identify them, as well as other parts of mRNA and tRNA, and to elucidate the structural determinants of their functions and interactions. Experimental results are presented that bear upon codon context effects, the role of tRNA structural features in aminoacyl-tRNA selection and in codon selection (reading-frame maintenance), determinants of tRNA identity, elongation factor suppressor mutants, and termination codon recognition by the ribosomal RNA of the small subunit. The examples presented illustrate the complexity of the decoding process and the interconnectedness of translational macromolecules in achieving specificity and accuracy in polypeptide synthesis.

Anticodon↗

PubMed1993

Molecular characterization of naturally occurring glycoprotein C-negative herpes simplex virus type 1.

We previously isolated glycoprotein C (gC)-negative herpes simplex virus type 1 (HSV-1) mutants, TN-1, TN-2 and TN-3, from a patient with recurrent herpetic keratitis at one-year intervals. In the present study, the molecular basis for the inability of these clinical isolates to express gC was examined. The nucleotide sequence of the gC gene of the TN-1 strain was compared with that of the HSV-1 KOS strain. In the open reading frame of the gC gene, there were 12 nucleotide differences between the TN-1 and KOS strains, seven of which led to amino acid substitutions. Importantly, one of them was the codon change from CAG for glutamine at position 280 to TAG for the amber termination codon. Accordingly, the TN-1 strain produced a truncated gC with a predicted molecular weight, which was secreted into the extracellular fluid. These results suggest that this amber mutation in the TN-gC gene results in a premature termination of gC translation and is the cause of the gC-negative phenotype of the TN strains. It is expected that these extremely rare HSV-1 strains will provide us with valuable information concerning the in vivo functions of gC, especially in ocular diseases.

Adult↗

PubMed1993

More potent transcriptional activators or a transdominant inhibitor of the HNF1 homeoprotein family are generated by alternative RNA processing.

We report the isolation of cDNAs from human liver encoding several isoforms of the hepatocyte nuclear factor homeoproteins HNF1 and vHNF1 generated by the differential use of polyadenylation sites and by alternative splicing. In the novel isoforms intron sequences that are excised in the previously described forms are translated in the same frame as exon sequences until the first termination codon is encountered. Hence, the newly found isoforms all contain different C-terminal domains. For HNF1 it has been shown that its C-terminal region is responsible for the activation of transcription. In transient transfection assays the two novel HNF1 isoforms, HNF1-B and -C, transactivate 5-fold better than the previously described HNF1 protein (HNF1-A). The newly isolated isoform of vHNF1, designated vHNF1-C, is unable to transactivate and behaves as a transdominant repressor when cotransfected with HNF1-A, -B or -C. All of the different isoforms of HNF1 and vHNF1 can form homo- and heterodimers and their mRNAs are differentially expressed in fetal and adult human liver, kidney and intestine, suggesting distinct roles during development. Our studies show that the transactivation domain of the members of the HNF1 homeoprotein family is organized in modules which can be exchanged to generate either more potent transcriptional activators or a transdominant repressor.

Alternative Splicing↗

PubMed1987

Cloning and sequencing of the HU-2 gene of Escherichia coli.

The Escherichia coli HU-2 gene was cloned using a DNA fragment from the HU-1 gene as a probe. The amino acid sequence of the HU-2 protein deduced from the nucleotide sequence is in good agreement with the published sequence. The nucleotide sequence has a possible promoter and a typical ribosomal binding site upstream of the translation initiation codon (AUG) and a possible rho-independent terminater site downstream of the termination codon (UAA) of the gene.

Amino Acid Sequence↗

PubMed2002

Characterization of pMa025, a plasmid from the cyanobacterium Microcystis aeruginosa UV025.

The characterization of pMa025, a plasmid isolated from the unicellular, toxin-producing cyanobacterium Microcystis aeruginosa UV025, is described. A recombinant plasmid, pMaL [pMa025-pBluescript II SK(-)] was constructed for mapping, sequencing, and development of shuttle vectors capable of transforming both Escherichia coli and M. aeruginosa. pMa025 is 8,018 bp in length and has a G+C content of 62.3 mol%. Nineteen presumptive ORFs, ORF A - ORF S were identified using ATG or GTG as initiation codons. Fifteen different ORFs, ORF a - ORF o were identified using TGA as a degenerate codon for tryptophan. GTG was the start codon in two-thirds of the putative ORFs when TGA was the termination codon. GTG was the start codon in one-third of the putative ORFs when TGA was used as a codon for tryptophan. The deduced amino acid sequence from ORF j (3,114 bp) was significantly similar to that of a putative plasmid replication protein, RepA, from plasmid pUH24 of Synecho coccus sp. strain PCC7942. M. aeruginosa UV027 and E. coli were transformed to carbenicillin resistance with pMaL-D7, a 6.4-kb hybrid plasmid (3.46 kb pMa025, 2.95 kb pBluescript II) generated from the nested deletion strategy. pMaL-D7 will be used as a shuttle vector.

Base Sequence↗