Oka varicella vaccine is distinguishable from its parental virus in DNA sequence of open reading frame 62 and its transactivation activity

Saccharomyces cerevisiae Ty elements are transposons closely related to retroviruses. The DNA sequence of a functional Ty element (TyH3) is presented. The long terminal repeat sequences are different, suggesting that TyH3 is a recombinant Ty element. A chromosomal Ty element near the LYS2 gene, Ty173, was found to be nonfunctional, even though it has no detectable insertions or deletions. The defect in Ty173 transposition is caused by a missense mutation giving rise to a Leu-to-Ile substitution in the TYB (pol) open reading frame. Several chromosomal Ty elements carry this lesion in their DNA, indicating that nonfunctional Ty elements are common in the yeast genome.

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DNA sequence and transcript mapping of MOD5: features of the 5' region which suggest two translational starts

Molecular and Cellular Biology ◽

10.1128/mcb.7.1.185-191.1987 ◽

1987 ◽

Vol 7 (1) ◽

pp. 185-191

Author(s):

D Najarian ◽

M E Dihanich ◽

N C Martin ◽

A K Hopper

Keyword(s):

Dna Sequence ◽

Nuclear Gene ◽

Open Reading Frame ◽

Isopentenyl Transferase ◽

Gene Encoding ◽

Reading Frame ◽

Amino Terminal ◽

Initiation Of Translation ◽

Cellular Compartments ◽

Lines Of Evidence

A mutation in the yeast nuclear gene MOD5 drastically reduces the biosynthesis of the modified base isopentenyladenosine in tRNAs located in different cellular compartments: the mitochondria and the nucleus or cytoplasm. Several lines of evidence strongly suggest that MOD5 is the structural gene encoding the tRNA-modifying enzyme delta 2-isopentenyl pyrophosphate:tRNA isopentenyl transferase. DNA sequence analysis of MOD5 reveals an open reading frame of 428 amino acids. A set of mRNAs heterogeneous at both the 5' and 3' termini are transcribed from this gene. Although all of these transcripts initiate upstream of the first AUG codon of the open reading frame, a subset has an extremely short (greater than or equal to 1 base) 5' leader. Furthermore, in positions important for efficient initiation of translation and generally occupied by purines, this first AUG codon is flanked by a U (position -3) and a C (position +4). It is possible that two proteins, one with an amino-terminal extension of basic charge, could be generated from the MOD5 gene via differential translational starts.

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A highly conserved mouse gene with a propensity to form pseudogenes in mammals.

Molecular and Cellular Biology ◽

10.1128/mcb.8.7.2797 ◽

1988 ◽

Vol 8 (7) ◽

pp. 2797-2803 ◽

Cited By ~ 25

Author(s):

D L Heller ◽

K M Gianola ◽

L A Leinwand

Keyword(s):

Dna Sequence ◽

Cdna Clone ◽

Restriction Analysis ◽

In Vitro Transcription ◽

Open Reading Frame ◽

Cdna Clones ◽

Reading Frame ◽

Mouse Cdna ◽

Processed Pseudogenes

A mouse cDNA clone corresponding to an abundantly transcribed poly(A)+ mRNA was found to be represented by 200 copies in mammalian genomes. To understand the origin and nature of this sequence family, we studied two genomic members and two cDNA clones from mouse liver. The DNA sequence of the coding strand of a full-length cDNA clone was shown to have an open reading frame capable of encoding a 25-kilodalton polypeptide that has not been previously described. In vitro transcription-translation experiments verified the presence of an open reading frame encoding a protein of the predicted size. Restriction analysis of genomic DNA and DNA sequence analysis of genomic clones indicated that many of the 200 members of this family represent processed pseudogenes, with one or a small number of active structural genes. The vast majority of the genomic copies are heterogeneous in length, truncated at their 5' ends with respect to the mRNA, and do not appear to have intervening sequences. Two distinct genomic members of this family were sequenced and found to represent incomplete copies of the mRNA. Both are 5' truncated at slightly different points with respect to the mRNA. Both pseudogenes have multiple base changes, insertions, and deletions relative to the mRNA, and one of them encodes the poly(A) tail of the mRNA. The expression of this gene family is highest in rapidly dividing cells such as early mouse embryos and testis, but was seen in all tissues tested. This gene shows extremely high sequence conservation, extending to chicken, amphibian, and nematode genomes. Surprisingly, the gene appears to exist in only one copy in these organisms.

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The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1.

Molecular and Cellular Biology ◽

10.1128/mcb.8.4.1432 ◽

1988 ◽

Vol 8 (4) ◽

pp. 1432-1442 ◽

Cited By ~ 70

Author(s):

J D Boeke ◽

D Eichinger ◽

D Castrillon ◽

G R Fink

Keyword(s):

Saccharomyces Cerevisiae ◽

Long Terminal Repeat ◽

Missense Mutation ◽

Dna Sequence ◽

Open Reading Frame ◽

Yeast Genome ◽

Reading Frame ◽

Ty Elements ◽

Ty Element ◽

Repeat Sequences

Saccharomyces cerevisiae Ty elements are transposons closely related to retroviruses. The DNA sequence of a functional Ty element (TyH3) is presented. The long terminal repeat sequences are different, suggesting that TyH3 is a recombinant Ty element. A chromosomal Ty element near the LYS2 gene, Ty173, was found to be nonfunctional, even though it has no detectable insertions or deletions. The defect in Ty173 transposition is caused by a missense mutation giving rise to a Leu-to-Ile substitution in the TYB (pol) open reading frame. Several chromosomal Ty elements carry this lesion in their DNA, indicating that nonfunctional Ty elements are common in the yeast genome.

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The Varicella-Zoster Virus Open Reading Frame 63 Latency-Associated Protein Is Critical for Establishment of Latency

Journal of Virology ◽

10.1128/jvi.78.21.11833-11840.2004 ◽

2004 ◽

Vol 78 (21) ◽

pp. 11833-11840 ◽

Cited By ~ 42

Author(s):

Jeffrey I. Cohen ◽

Edward Cox ◽

Lesley Pesnicak ◽

Shamala Srinivas ◽

Tammy Krogmann

Keyword(s):

Varicella Zoster Virus ◽

Dorsal Root Ganglia ◽

Dorsal Root ◽

Mutant Virus ◽

Open Reading Frame ◽

Parental Virus ◽

Reading Frame ◽

Varicella Zoster ◽

Latently Infected

ABSTRACT Varicella-zoster virus (VZV) expresses at least six viral transcripts during latency. One of these transcripts, derived from open reading frame 63 (ORF63), is one of the most abundant viral RNAs expressed during latency. The VZV ORF63 protein has been detected in human and experimentally infected rodent ganglia by several laboratories. We have deleted >90% of both copies of the ORF63 gene from the VZV genome. Animals inoculated with the ORF63 mutant virus had lower mean copy numbers of latent VZV genomes in the dorsal root ganglia 5 to 6 weeks after infection than animals inoculated with parental or rescued virus, and the frequency of latently infected animals was significantly lower in animals infected with the ORF63 mutant virus than in animals inoculated with parental or rescued virus. In contrast, the frequency of animals latently infected with viral mutants in other genes that are equally or more impaired for replication in vitro, compared with the ORF63 mutant, is similar to that of animals latently infected with parental VZV. Examination of dorsal root ganglia 3 days after infection showed high levels of VZV DNA in animals infected with either ORF63 mutant or parental virus; however, by days 6 and 10 after infection, the level of viral DNA in animals infected with the ORF63 mutant was significantly lower than that in animals infected with parental virus. Thus, ORF63 is not required for VZV to enter ganglia but is the first VZV gene shown to be critical for establishment of latency. Since the present vaccine can reactivate and cause shingles, a VZV vaccine based on the ORF63 mutant virus might be safer.

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The rIIA gene of bacteriophage T4. I. Its DNA sequence and discovery of a new open reading frame between genes 60 and rIIA.

Genetics ◽

10.1093/genetics/125.2.237 ◽

1990 ◽

Vol 125 (2) ◽

pp. 237-248

Author(s):

P Daegelen ◽

E Brody

Keyword(s):

Dna Sequence ◽

Bacteriophage T4 ◽

Regulation Of Gene Expression ◽

High Sensitivity ◽

Open Reading Frame ◽

Reading Frame ◽

Molecular Weights ◽

Control Regulation ◽

Small Open Reading Frame ◽

Repeated Motif

Abstract We have determined the DNA sequence of the rIIA gene and have discovered a small open reading frame, rIIA.1, between genes 60 and rIIA. The predicted molecular weights of these proteins are 82,840 for rIIA and 8,124 for rIIA.1. The rIIA protein has a repeated motif which suggests that the gene has evolved by duplication. It also has a motif which suggests that it belongs to a group of ompR-like proteins that control regulation of gene expression in response to changes in the external environment. We have sequenced three different missense mutants whose mutations lie in the Ala segment of the rIIA genetic map. All three changes are found within the first 35 bp of the rIIA coding sequence. The region of control of protein synthesis is identical in the rIIA gene and in gene 44 of T4. We relate this finding to the high sensitivity of both RNAs to translational repression by the T4 regA gene product.

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Improved Identification and Differentiation of Varicella-Zoster Virus (VZV) Wild-Type Strains and an Attenuated Varicella Vaccine Strain Using a VZV Open Reading Frame 62-Based PCR

Journal of Clinical Microbiology ◽

10.1128/jcm.38.9.3156-3160.2000 ◽

2000 ◽

Vol 38 (9) ◽

pp. 3156-3160 ◽

Cited By ~ 70

Author(s):

Vladimir N. Loparev ◽

Takele Argaw ◽

Philip R. Krause ◽

Michiko Takayama ◽

D. Scott Schmid

Keyword(s):

Varicella Zoster Virus ◽

Vaccine Strain ◽

Varicella Vaccine ◽

Open Reading Frame ◽

Cleavage Sites ◽

Wild Type ◽

Reading Frame ◽

Varicella Zoster ◽

Enzyme Cleavage ◽

Type Strains

A new method was developed to identify and differentiate varicella-zoster virus (VZV) wild-type strains from the attenuated varicella Oka vaccine strain. The PCR technique was used to amplify a VZV open reading frame (ORF) 62 region. A single specific amplicon of 268 bp was obtained from 71 VZV clinical isolates and several laboratory strains. Subsequent digestion of the VZV ORF 62 amplicons with SmaI enabled accurate strain differentiation (threeSmaI sites were present in amplicons of vaccine strain VZV, compared with two enzyme cleavage sites for all other VZV strains tested). This method accurately differentiated the Oka vaccine strain from wild-type VZV strains circulating in countries representing all six populated continents. Moreover, the assay more reliably distinguished wild-type Japanese strains from the vaccine strain than did previously described methods.

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A highly conserved mouse gene with a propensity to form pseudogenes in mammals

Molecular and Cellular Biology ◽

10.1128/mcb.8.7.2797-2803.1988 ◽

1988 ◽

Vol 8 (7) ◽

pp. 2797-2803

Author(s):

D L Heller ◽

K M Gianola ◽

L A Leinwand

Keyword(s):

Dna Sequence ◽

Cdna Clone ◽

Restriction Analysis ◽

In Vitro Transcription ◽

Open Reading Frame ◽

Cdna Clones ◽

Reading Frame ◽

Mouse Cdna ◽

Processed Pseudogenes

A mouse cDNA clone corresponding to an abundantly transcribed poly(A)+ mRNA was found to be represented by 200 copies in mammalian genomes. To understand the origin and nature of this sequence family, we studied two genomic members and two cDNA clones from mouse liver. The DNA sequence of the coding strand of a full-length cDNA clone was shown to have an open reading frame capable of encoding a 25-kilodalton polypeptide that has not been previously described. In vitro transcription-translation experiments verified the presence of an open reading frame encoding a protein of the predicted size. Restriction analysis of genomic DNA and DNA sequence analysis of genomic clones indicated that many of the 200 members of this family represent processed pseudogenes, with one or a small number of active structural genes. The vast majority of the genomic copies are heterogeneous in length, truncated at their 5' ends with respect to the mRNA, and do not appear to have intervening sequences. Two distinct genomic members of this family were sequenced and found to represent incomplete copies of the mRNA. Both are 5' truncated at slightly different points with respect to the mRNA. Both pseudogenes have multiple base changes, insertions, and deletions relative to the mRNA, and one of them encodes the poly(A) tail of the mRNA. The expression of this gene family is highest in rapidly dividing cells such as early mouse embryos and testis, but was seen in all tissues tested. This gene shows extremely high sequence conservation, extending to chicken, amphibian, and nematode genomes. Surprisingly, the gene appears to exist in only one copy in these organisms.

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Identification and Characterization of thescl Gene Encoding a Group A StreptococcusExtracellular Protein Virulence Factor with Similarity to Human Collagen

Infection and Immunity ◽

10.1128/iai.68.12.6542-6553.2000 ◽

2000 ◽

Vol 68 (12) ◽

pp. 6542-6553 ◽

Cited By ~ 119

Author(s):

Slawomir Lukomski ◽

Kazumitsu Nakashima ◽

Iman Abdi ◽

Vincent J. Cipriano ◽

Robin M. Ireland ◽

...

Keyword(s):

Amino Acid ◽

Dna Sequence ◽

Structural Gene ◽

Virulence Factor ◽

Open Reading Frame ◽

Genomic Diversity ◽

Reading Frame ◽

Isogenic Mutant ◽

Group A ◽

Human Collagen

ABSTRACT Group A Streptococcus (GAS) expresses cell surface proteins that mediate important biological functions such as resistance to phagocytosis, adherence to plasma and extracellular matrix proteins, and degradation of host proteins. An open reading frame encoding a protein of 348 amino acid residues was identified by analysis of the genome sequence available for a serotype M1 strain. The protein has an LPATGE sequence located near the carboxy terminus that matches the consensus sequence (LPXTGX) present in many gram-positive cell wall-anchored molecules. Importantly, the central region of this protein contains 50 contiguous Gly-X-X triplet amino acid motifs characteristic of the structure of human collagen. The structural gene (designated scl for streptococcal collagen-like) was present in all 50 GAS isolates tested, which together express 21 different M protein types and represent the breadth of genomic diversity in the species. DNA sequence analysis of the gene in these 50 isolates found that the number of contiguous Gly-X-X motifs ranged from 14 in serotype M6 isolates to 62 in a serotype M41 organism. M1 and M18 organisms had the identical allele, which indicates very recent horizontal gene transfer. The gene was transcribed abundantly in the logarithmic but not stationary phase of growth, a result consistent with the occurrence of a DNA sequence with substantial homology with a consensus Mga binding site immediately upstream of the sclopen reading frame. Two isogenic mutant M1 strains created by nonpolar mutagenesis of the scl structural gene were not attenuated for mouse virulence as assessed by intraperitoneal inoculation. In contrast, the isogenic mutant derivative made from the M1 strain representative of the subclone most frequently causing human infections was significantly less virulent when inoculated subcutaneously into mice. In addition, both isogenic mutant strains had significantly reduced adherence to human A549 epithelial cells grown in culture. These studies identify a new extracellular GAS virulence factor that is widely distributed in the species and participates in adherence to host cells and soft tissue pathology.

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