Analysis of Early Promoters of theBacillus Bacteriophage GA-1

ABSTRACT Bacteriophage GA-1, which infects Bacillus sp. strain G1R, is evolutionarily related to phage φ29, which infectsBacillus subtilis. We report the characterization of several GA-1 promoters located at either end of its linear genome. Some of them are unique for GA-1 and drive the expression of open reading frames that have no counterparts in the genome of φ29 or related phages. These unique promoters are active at early infection times and are repressed at late times. In vitro transcription reactions revealed that the purified GA-1-encoded protein p6 represses the activity of these promoters, although the amount of p6 required to repress transcription was different for each promoter. The level of protein p6 produced in vivo increases rapidly during the first stage of the infection cycle. The protein p6 concentration may serve to modulate the expression of these early promoters as infection proceeds.

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Characterization of Endogenous Retroviruses in Sheep

Journal of Virology ◽

10.1128/jvi.77.20.11268-11273.2003 ◽

2003 ◽

Vol 77 (20) ◽

pp. 11268-11273 ◽

Cited By ~ 14

Author(s):

Nikolai Klymiuk ◽

Mathias Müller ◽

Gottfried Brem ◽

Bernhard Aigner

Keyword(s):

Endogenous Retrovirus ◽

Ovis Aries ◽

Endogenous Retroviruses ◽

Open Reading Frames ◽

In Vivo Experiments ◽

Pregnant Sheep ◽

Reading Frames

ABSTRACT Endogenous retrovirus (ERV) sequences have been found in all mammals. In vitro and in vivo experiments revealed ERV activation and cross-species infection in several species. Sheep (Ovis aries) are used for various biotechnological purposes; however, they have not yet been comprehensively screened for ERV sequences. Therefore, the aim of the study was to classify the ERV sequences in the ovine genome (OERV) by analyzing the retroviral pro-pol sequences. Three OERV β families and nine OERV γ families were revealed. Novel open reading frames (ORF) in the amplified proviral fragment were found in one OERV β family and two OERV γ families. Hybrid OERV produced by putative recombination events were not detected. Quantitative analysis of the OERV sequences in the ovine genome revealed no relevant variations in the endogenous retroviral loads of different breeds. Expression analysis of different tissues from fetal and pregnant sheep detected mRNA from both gammaretrovirus families, showing ORF fragments. Thus, the release of retroviruses from sheep cells cannot be excluded.

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Characterization of the Pasteurella multocida hgbA Gene Encoding a Hemoglobin-Binding Protein

Infection and Immunity ◽

10.1128/iai.70.11.5955-5964.2002 ◽

2002 ◽

Vol 70 (11) ◽

pp. 5955-5964 ◽

Cited By ~ 22

Author(s):

Montserrat Bosch ◽

M. Elena Garrido ◽

Montserrat Llagostera ◽

Ana M. Pérez de Rozas ◽

Ignacio Badiola ◽

...

Keyword(s):

Pasteurella Multocida ◽

Bacterial Pathogen ◽

Open Reading Frames ◽

Transcriptional Unit ◽

Gene Encoding ◽

Hemoglobin Binding ◽

Reading Frames

ABSTRACT Reverse transcriptase PCR analyses have demonstrated that open reading frames (ORFs) PM0298, PM0299, and PM0300 of the animal pathogen Pasteurella multocida constitute a single transcriptional unit. By cloning and overexpression studies in Escherichia coli cells, the product of ORF PM0300 was shown to bind hemoglobin in vitro; this ORF was therefore designated hgbA. In vitro and in vivo quantitative assays demonstrated that the P. multocida hgbA mutant bound hemoglobin to the same extent as the wild-type strain, although the adsorption kinetics was slightly slower for the hgbA cells. In agreement with this, the virulence of P. multocida hgbA cells was not affected, suggesting that other functional hemoglobin receptor proteins must be present in this organism. On the other hand, P. multocida mutants defective in PM0298 and PM0299 could be isolated only when a plasmid containing an intact copy of the gene was present in the cells, suggesting that these genes are essential for the viability of this bacterial pathogen. By adapting the recombinase-based expression technology in vivo to P. multocida, we also demonstrated that the transcriptional PM0298-PM0299-hgbA unit is iron regulated and that its expression is triggered in the first 2 h following infection in a mouse model. Furthermore, hybridization experiments showed that the hgbA gene is widespread in P. multocida strains regardless of their serotype or the animal from which they were isolated.

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MOLECULAR CHARACTERIZATION OF A NOVEL RAT PARVOVIRUS IN TAIWAN

Taiwan Veterinary Journal ◽

10.1142/s1682648514500024 ◽

2014 ◽

Vol 40 (01) ◽

pp. 11-19 ◽

Cited By ~ 1

Author(s):

Yi-Chun Liao ◽

Ming-Hseng Wang ◽

Cho-Hua Wan

Keyword(s):

Molecular Characterization ◽

Open Reading Frames ◽

Infectious Agents ◽

Sequence Comparisons ◽

Laboratory Rats ◽

Laboratory Rodents ◽

Reading Frames

Rodent parvoviruses are among the most prevalent infectious agents in laboratory rodents and have been shown to interfere with in vivo and in vitro research. A newly recognized rat parvovirus (RPV) that is distinct from the prototypic RPV was recently identified in naturally infected laboratory rats in Taiwan. Nucleotide and amino acid sequence comparisons showed that this newly identified variant of RPV is most closely related to rat parvovirus type 1a (RPV-1a) and type 1b (RPV-1b) and is distinctly different from type UT (RPV/UT) and other rodent parvoviruses. This variant was designated rat parvovirus type National Taiwan University 1 (RPV-NTU1). Phylogenetic and sequence analyses revealed that RPV-NTU1 contains conserved open reading frames with an overall genome organization similar to known RPV-1. RPV-NTU1 is the second RPV-1 variant whose full-length molecular characterization has been performed.

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Genomic Sequence of Rhesus Cytomegalovirus 180.92: Insights into the Coding Potential of Rhesus Cytomegalovirus

Journal of Virology ◽

10.1128/jvi.80.8.4179-4182.2006 ◽

2006 ◽

Vol 80 (8) ◽

pp. 4179-4182 ◽

Cited By ~ 50

Author(s):

Pierre Rivailler ◽

Amitinder Kaur ◽

R. Paul Johnson ◽

Fred Wang

Keyword(s):

Genomic Sequence ◽

Open Reading Frames ◽

Rhesus Cytomegalovirus ◽

Human Cmv ◽

Coding Capacity ◽

Coding Potential ◽

Reading Frames ◽

Genetic Rearrangements

ABSTRACT A pathogenic isolate of rhesus cytomegalovirus (rhCMV 180.92) was cloned, sequenced, and annotated. Comparisons with the published rhCMV 68.1 genome revealed 8 open reading frames (ORFs) in isolate 180.92 that are absent in 68.1, 10 ORFs in 68.1 that are absent in 180.92, and 34 additional ORFs that were not previously annotated. Most of the differences appear to be due to genetic rearrangements in both isolates from a region that is frequently altered in human CMV (hCMV) during in vitro passage. These results indicate that the rhCMV ORF repertoire is larger than previously recognized. Like hCMV, understanding of the complete coding capacity of rhCMV is complicated by genomic instability and may require comparisons with additional isolates in vitro and in vivo.

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E1−E4+ Adenoviral Gene Transfer Vectors Function as a “Pro-Life” Signal to Promote Survival of Primary Human Endothelial Cells

Blood ◽

10.1182/blood.v93.9.2936 ◽

1999 ◽

Vol 93 (9) ◽

pp. 2936-2944 ◽

Cited By ~ 22

Author(s):

Ramachandran Ramalingam ◽

Shahin Rafii ◽

Stefan Worgall ◽

Douglas E. Brough ◽

Ronald G. Crystal

Keyword(s):

Endothelial Cells ◽

Open Reading Frames ◽

Adenoviral Gene Transfer ◽

Vector Genome ◽

Transfer Vectors ◽

Reading Frames ◽

Human Endothelium ◽

Pro Life

Abstract Although endothelial cells are quiescent and long-lived in vivo, when they are removed from blood vessels and cultured in vitro they die within days to weeks. In studies of the interaction of E1−E4+ replication–deficient adenovirus (Ad) vectors and human endothelium, the cells remained quiescent and were viable for prolonged periods. Evaluation of these cultures showed that E1−E4+ Ad vectors provide an “antiapoptotic” signal that, in association with an increase in the ratio of Bcl2 to Bax levels, induces the endothelial cells to enter a state of “suspended animation,” remaining viable for at least 30 days, even in the absence of serum and growth factors. Although the mechanisms initiating these events are unclear, the antiapoptoic signal requires the presence of E4 genes in the vector genome, suggesting that one or more E4 open reading frames of subgroup C Ad initiate a “pro-life” program that modifies cultured endothelial cells to survive for prolonged periods.

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An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.14.7.4485 ◽

1994 ◽

Vol 14 (7) ◽

pp. 4485-4492 ◽

Cited By ~ 56

Author(s):

B A Dombroski ◽

Q Feng ◽

S L Mathias ◽

D M Sassaman ◽

A F Scott ◽

...

Keyword(s):

Reverse Transcriptase ◽

Consensus Sequence ◽

Unknown Origin ◽

Open Reading Frames ◽

Long Terminal Repeats ◽

Base Pairs ◽

In Vivo Assay ◽

Reading Frames

L1 elements constitute a highly repetitive human DNA family (50,000 to 100,000 copies) lacking long terminal repeats and ending in a poly(A) tail. Some L1 elements are capable of retrotransposition in the human genome (Kazazian, H. H., Jr., C. Wong, H. Youssoufian, A. F. Scott, D. G. Phillips, and S.E. Antonarakis, Nature (London) 332:164-166, 1988). Although most are 5' truncated, a consensus sequence of complete L1 elements is 6 kb long and contains two open reading frames (ORFs) (Scott, A. F., B. J. Schmeckpeper, M. Abdelrazik, C. T. Comey, B. O'Hara, J. P. Rossiter, T. Cooley, P. Health, K. D. Smith, and L. Margolet, Genomics 1:113-125, 1987). The protein encoded by ORF2 has reverse transcriptase (RT) activity in vitro (Mathias, S. L., A. F. Scott, H. H. Kazazian, Jr., J. D. Boeke, and A. Gabriel, Science 254:1808-1810, 1991). Because L1 elements are so numerous, efficient methods for identifying active copies are required. We have developed a simple in vivo assay for the activity of L1 RT based on the system developed by Derr et al. (Derr, L. K., J. N. Strathern, and D. J. Garfinkel, Cell 67:355-364, 1991) for yeast HIS3 pseudogene formation. L1 ORF2 displays an in vivo RT activity similar to that of yeast Ty1 RT in this system and generates pseudogenes with unusual structures. Like the HIS3 pseudogenes whose formation depends on Ty1 RT, the HIS3 pseudogenes generated by L1 RT are joined to Ty1 sequences and often are part of complex arrays of Ty1 elements, multiple HIS3 pseudogenes, and hybrid Ty1/L1 elements. These pseudogenes differ from those previously described in that there are base pairs of unknown origin inserted at several of the junctions. In two of three HIS3 pseudogenes studied, the L1 RT appears to have jumped from the 5' end of a Ty1/L1 transcript to the poly(A) tract of the HIS3 RNA.

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Genetic Localization and Molecular Characterization of the nonS Gene Required for Macrotetrolide Biosynthesis inStreptomyces griseus DSM40695

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.44.7.1809-1817.2000 ◽

2000 ◽

Vol 44 (7) ◽

pp. 1809-1817 ◽

Cited By ~ 38

Author(s):

Wyatt C. Smith ◽

Longkuan Xiang ◽

Ben Shen

Keyword(s):

Polyketide Synthase ◽

Isotope Labeling ◽

Streptomyces Griseus ◽

Open Reading Frames ◽

A Cell ◽

Cyclic Polyethers ◽

The Difference ◽

Reading Frames

ABSTRACT The macrotetrolides are a family of cyclic polyethers derived from tetramerization, in a stereospecific fashion, of the enantiomeric nonactic acid (NA) and its homologs. Isotope labeling experiments established that NA is of polyketide origin, and biochemical investigations demonstrated that 2-methyl-6,8-dihydroxynon-2E-enoic acid can be converted into NA by a cell-free preparation from Streptomyces lividans that expresses nonS. These results lead to the hypothesis that macrotetrolide biosynthesis involves a pair of enantiospecific polyketide pathways. In this work, a 55-kb contiguous DNA region was cloned from Streptomyces griseus DSM40695, a 6.3-kb fragment of which was sequenced to reveal five open reading frames, including the previously reported nonR andnonS genes. Inactivation of nonS in vivo completely abolished macrotetrolide production. Complementation of thenonS mutant by the expression of nonS intrans fully restored its macrotetrolide production ability, with a distribution of individual macrotetrolides similar to that for the wild-type producer. In contrast, fermentation of thenonS mutant in the presence of exogenous (±)-NA resulted in the production of nonactin, monactin, and dinactin but not in the production of trinactin and tetranactin. These results prove the direct involvement of nonS in macrotetrolide biosynthesis. The difference in macrotetrolide production between in vivo complementation of the nonS mutant by the plasmid-borne nonSgene and fermentation of the nonS mutant in the presence of exogenously added (±)-NA suggests that NonS catalyzes the formation of (−)-NA and its homologs, supporting the existence of a pair of enantiospecific polyketide pathways for macrotetrolide biosynthesis inS. griseus. The latter should provide a model that can be used to study the mechanism by which polyketide synthase controls stereochemistry during polyketide biosynthesis.

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Ancient Adversary – HERV-K (HML-2) in Cancer

Frontiers in Oncology ◽

10.3389/fonc.2021.658489 ◽

2021 ◽

Vol 11 ◽

Author(s):

Eoin Dervan ◽

Dibyangana D. Bhattacharyya ◽

Jake D. McAuliffe ◽

Faizan H. Khan ◽

Sharon A. Glynn

Keyword(s):

Tumour Progression ◽

Endogenous Retroviruses ◽

Open Reading Frames ◽

Human Endogenous Retroviruses ◽

Viral Particles ◽

Metastatic Capacity ◽

Coding Capacity ◽

Reading Frames

Human endogenous retroviruses (HERV), ancient integrations of exogenous viruses, make up 8% of our genome. Long thought of as mere vestigial genetic elements, evidence is now accumulating to suggest a potential functional role in numerous pathologies including neurodegenerative diseases, autoimmune disorders, and multiple cancers. The youngest member of this group of transposable elements is HERV-K (HML-2). Like the majority of HERV sequences, significant post-insertional mutations have disarmed HERV-K (HML-2), preventing it from producing infectious viral particles. However, some insertions have retained limited coding capacity, and complete open reading frames for all its constituent proteins can be found throughout the genome. For this reason HERV-K (HML-2) has garnered more attention than its peers. The tight epigenetic control thought to suppress expression in healthy tissue is lost during carcinogenesis. Upregulation of HERV-K (HML-2) derived mRNA and protein has been reported in a variety of solid and liquid tumour types, and while causality has yet to be established, progressively more data are emerging to suggest this phenomenon may contribute to tumour growth and metastatic capacity. Herein we discuss its potential utility as a diagnostic tool and therapeutic target in light of the current in vitro, in vivo and clinical evidence linking HERV-K (HML-2) to tumour progression.

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Translational activation of GCN4 mRNA in a cell-free system is triggered by uncharged tRNAs

Molecular and Cellular Biology ◽

10.1128/mcb.10.8.4375-4378.1990 ◽

1990 ◽

Vol 10 (8) ◽

pp. 4375-4378

Author(s):

G Krupitza ◽

G Thireos

Keyword(s):

Open Reading Frames ◽

Yeast Cells ◽

Free System ◽

In Vitro System ◽

A Cell ◽

Translational Activation ◽

Reading Frames ◽

Small Open Reading Frames

Translation of GCN4 mRNA is activated when yeast cells are grown under conditions of amino acid limitation. In this study, we established the conditions through which translation of the GCN4 mRNA could be activated in a homologous in vitro system. This activation paralleled the in vivo situation: it required the small open reading frames located in the 5' untranslated region of the GCN4 mRNA, and it was coupled with reduced rates of 43S preinitiation complex formation. Translational derepression in vitro was triggered by uncharged tRNA molecules, demonstrating that deacylated tRNAs are more proximal signals for translational activation of the GCN4 mRNA.

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