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Herpes simplex virus latency-associated transcript gene function.

A major area of interest in the study of herpes simplex virus type 1 (HSV-1) involves the persistence of the virus within a latent state in neuronal cells of infected humans. The latency-associated transcripts (LATs) are believed to play a key role during HSV-1 latency. This review will discuss the most recent findings on the involvement of the LAT region with apoptotic pathways and how this relates to other potential functions of the LATs.

Animals↗

A cell line for high-yield production of E1-deleted adenovirus vectors without the emergence of replication-competent virus.

Production of E1-deleted adenovirus vectors for gene therapy has been plagued by the emergence of replication-competent adenovirus. A number of investigators have minimized homologous sequences between the vector and transfected E1 DNA in an attempt to avoid replication-competent adenovirus. We describe a HeLa-based cell line called GH329 that stably expresses the E1 locus from a promoter derived from the phosphoglycerate kinase gene. Overlap sequences with a standard E1-deleted vector that retains a full pIX transcriptional unit have been eliminated at the 5' end and minimized at the 3' end. The GH329 cell line plaques and produces E1-deleted adenovirus as well as 293 cells. Replication-competent virus has emerged after 5 passages of vector on 293 cells but was not detected after 20 passages on GH329 cells.

Adenoviridae↗

Unexpected transcriptional signals in normal and mitotically defective cells mediated through cytokine and growth factor receptors.

Polypeptide growth factors and cytokines mediate their biochemical functions through their responsive receptors. Known cytokine receptors do not possess intrinsic kinase domains whereas several polypeptide growth factor receptors do. Nevertheless, both classes of ligands are capable of activating sets of overlapping genes. In human epidermoid carcinoma cells, for example, both cytokines and epidermal growth factor (EGF) promote a common transcriptional activation signal through the tyrosine phosphorylation of stat91 (signal transducer and activator of transcription) proteins. The stat family of cytoplasmic proteins also appear to have dual functions. Tyrosine phosphorylated 'stats' are employed for signal transduction and, second, for activation of transcription of several genes. The transcription factor-SIE-DNA binding patterns are now known to be different for EGF and interferon-gamma IFN-gamma-treated cells. Nevertheless, in the active DNA-bound complex, the stat91 polypeptide is a component found in either EGF or INF-gamma-treated extracts. Other stat family members of transcription factors may also be present in the complexes. In this case, tyrosine phosphorylated stat91 polypeptides may form into homodimeric or heterodimeric assemblies with other stat-related transcription factors. We describe a novel stat-related factor, p93, that is found in EGF-treated A431 cell extracts but appears to be absent in bovine fibroblast growth factor (bFGF), IFN-gamma, tumor necrosis factor-alpha (TNF-alpha), and untreated cells. p93 appears to be antigenically related to stat91. p185c-neu+, EGFr+ (M1), and p185c-neu- kinase inactive, EGFr+ (NEN757) expressing cells undergo different mitotic responses to EGF. M1 can respond to EGF mitotically while NEN757 cannot. Both cell lines respond to 10 ng/ml of EGF and also to IFN-gamma in transducing transcriptional activation signals to the nucleus, despite the distinct growth response to EGF. Our work has analyzed the stat pathway in these types of cells and found similar patterns of usage despite the distinct EGF-responsive features. Cytoplasmic nonreceptor tyrosine kinases Jak1 and Jak2 may be involved in the activation of stat91 and other transcription factors in EGF and IFN-gamma signaling pathways. Collectively, these studies suggest that the major EGF-stimulated mitotic growth pathways may not be absolutely linked to the stat91 signaling pathways and that such transcription complexes are more complex than previously reported.

Animals↗

Isolation and characterization of the fission yeast protein phosphatase gene ppe1+ involved in cell shape control and mitosis.

We isolated a fission yeast putative protein serine/threonine phosphatase gene designated ppe1+ by hybridization. The predicted amino acid sequence is similar to those of the fission yeast ppa2 (53% identity) and dis2 (39%) phosphatases, and highly similar to those of the budding yeast SIT4 (72%), Drosophila PPV (68%) and rabbit PPX (61%) phosphatases. Antibodies against ppe1 protein identified a 37-kd polypeptide in fission yeast. A gene disruption (designated delta ppe1) caused cold-sensitive lethality and short, pear-shaped cells. These phenotypes were fully suppressed by a plasmid carrying ppe1+. Three classes of multicopy suppressor genes for delta ppe1 were identified as follows: 1) ppa1+ and ppa2+ encoding type 2A-like phosphatases, 2) mitotically essential dis3+ similar to the budding yeast SSD1/SRK1, a suppressor for sit4, and 3) pck1+ coding for a protein kinase C-like kinase. Consistently, the budding yeast SIT4 gene was also a multicopy suppressor for delta ppe1. Phosphatase ppe1 may play a role in cell morphogenesis and mitosis by either regulating or being regulated by these multicopy suppressor gene products. Consistent with this hypothesis, double mutants ppe1-ppa2 and ppe1-pck1 are lethal at the permissive temperature.

Amino Acid Sequence↗

Expression of the ORF-2 protein of the human respiratory syncytial virus M2 gene is initiated by a ribosomal termination-dependent reinitiation mechanism.

Translation of the open reading frame 2 (ORF-2) of the human respiratory syncytial virus M2 gene initiates at one of the three initiation codons located upstream of the termination codon for the first ORF. Replacement of ORF-2 with the major ORF of the chloramphenicol acetyltransferase reporter gene followed by systematic mutagenesis of the putative initiation codons demonstrated the usage of these codons as the translational initiators for ORF-2 expression both in vitro and in vivo. While the efficiency of translation was maintained when only the first and second AUG codons were preserved in vivo, there was no apparent preference in vitro for any of the three codons when only one was present. Mutagenesis studies showed that the location of the termination codon of ORF-1 protein plays a crucial role in directing translation of ORF-2 from the upstream initiation codons in vivo. This indicates that the second ORF is accessed by the ribosomes that are departing from the first ORF and that these ribosomes reinitiate on AUG codons 5' to the point of translation termination.

Base Sequence↗

The value of structural variants to conservation genomics in the pangenome era.

Structural variants (SVs) comprise an axis of genetic diversity with strong consequences for phenotype and fitness, making them a potentially important target for conservation genomics. Here, we review how and why SVs can play a role in conservation genomics; the different types of SVs and how they can affect phenotype; and how pangenomes and long-read sequencing are illuminating their evolution in populations, including small populations and those of conservation concern. SVs comprise multinucleotide mutations including insertions, deletions, transpositions, inversions, and other multinucleotide mutations, often overlapping genes and other functional genome regions. As a result, SVs often play important roles in phenotypic evolution and local adaptation and can contribute substantially to genetic load in inbred populations. However, our understanding of the factors influencing SV diversity in populations is still in its infancy and is complicated by the vast range of sizes, effects, and mechanisms of formation of these mutations. We argue that SVs are an important axis of genetic diversity which should be characterized alongside more traditional metrics of genetic diversity in conservation contexts. There are a number of analytical challenges to detecting and studying SVs, but analyses aimed at understanding the role of SVs in inbreeding load and population health are rapidly becoming realizable goals, accelerated by new technologies and analytical approaches. New tools, including population-scale long-read sequencing and pangenome approaches, are beginning to make SVs accessible in ways which can be readily applied in conservation settings.

Genomic Structural Variation↗

Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins.

We have successfully linked protein library screening directly with the identification of active proteins, without the need for individual purification, display technologies or physical linkage between the protein and its encoding sequence. By using 'MAX' randomization we have rapidly constructed 60 overlapping gene libraries that encode zinc finger proteins, randomized variously at the three principal DNA-contacting residues. Expression and screening of the libraries against five possible target DNA sequences generated data points covering a potential 40,000 individual interactions. Comparative analysis of the resulting data enabled direct identification of active proteins. Accuracy of this library analysis methodology was confirmed by both in vitro and in vivo analyses of identified proteins to yield novel zinc finger proteins that bind to their target sequences with high affinity, as indicated by low nanomolar apparent dissociation constants.

Binding Sites↗

A maturase-encoding group III twintron is conserved in deeply rooted euglenoid species: are group III introns the chicken or the egg?

The fourth intron of the Euglena gracilis chloroplast photosystem II gene, psbCi4, is a 1,605-bp twintron composed of two group III introns and a coding locus for a 458-aa polypeptide, mat1, located in the internal intron. psbCi4 homologs have been identified in seven euglenoids, including E. myxocylindracea, E. viridis, E. deses, E. pisciformis, Cryptoglena pigra, Eutreptia sp., and Lepocinclis beutschlii. All of the species examined contain both the group III twintron and the mat1 locus, revealing a more widespread occurrence of group III introns than previously known. The L. beutschlii mat1 locus is interrupted by two novel mini-group II introns of 224 and 258 nt, the smallest group II introns yet identified. Reverse transcriptase polymerase chain reaction analysis confirmed the splicing boundaries of the external and internal E. myxocylindracea, E. viridis, and E. deses introns as well as the novel L. beutschlii mat1 introns. As determined by comparative phylogenetic analysis, group III introns contain a structural homolog of group II intron domain VI. The mat1 loci encode peptide motifs characteristic of group II intron maturases. A group III intron-encoded protein whose predicted sequence is similar to group II intron-encoded maturases and a bona fide domain VI within group III introns are compelling evidence for a common ancestor of group II and group III introns.

Amino Acid Sequence↗

Nephron induction revisited: from caps to condensates.

Conversion of mesenchyme to epithelium in the metanephric kidney is clearly a multimolecular, multistep and partly redundant process. The present short review focuses on a neglected morphological aspect of kidney differentiation: the development of two transitory mesenchymal condensations that precede epithelial differentiation of nephrons. The first appearing condensate covers the tips of the collecting ducts and is termed a cap condensate. In the early kidney rudiment this structure has been referred to as a primary or early condensate. A few cells of the cap condensate (maybe only four to six cells), situated at the lateral edge of the cap, start proliferating rapidly and form a pretubular aggregate (or pretubular condensate), which converts to secretory nephron epithelia and finally segregates to different tubule segments. Throughout nephrogenesis, the cap condensates and pretubular aggregates are clearly distinguishable structures that show only partly overlapping gene expression profiles. Apart from being the source for the pretubular aggregates, the role of the cap condensate is unknown. It is now proposed that the cap regulates ureteric branching morphogenesis.

Animals↗

Structural aspects of proton-pumping ATPases.

ATP synthase is found in bacteria, chloroplasts and mitochondria. The simplest known example of such an enzyme is that in the eubacterium Escherichia coli; it is a membrane-bound assembly of eight different polypeptides assembled with a stoichiometry of alpha 3 beta 3 gamma 1 delta 1 epsilon 1 a1b2c10-12. The first five of these constitute a globular structure, F1-ATPase, which is bound to an intrinsic membrane domain, F0, an assembly of the three remaining subunits. ATP synthases driven by photosynthesis are slightly more complex. In chloroplasts, and probably in photosynthetic bacteria, they have nine subunits, all homologues of the components of the E. coli enzyme; the additional subunit is a duplicated and diverged relation of subunit b. The mammalian mitochondrial enzyme is more complex. It contains 14 different polypeptides, of which 13 have been characterized. Two membrane components, a (or ATPase-6) and A6L, are encoded in the mitochondrial genome in overlapping genes and the remaining subunits are nuclear gene products that are translated on cytoplasmic ribosomes and then imported into the organelle. The sequence of the proteins of ATP-synthase have provided information about amino acids that are important for its function. For example, amino acids contributing to nucleotide binding sites have been identified. Also, they provide the basis of models of secondary structure of membrane components that constitute the transmembrane proton channel. An understanding of the coupling of the transmembrane potential gradient for protons, delta mu H+, to ATP synthesis will probably require the determination of the structure of the entire membrane bound complex. Crystals have been obtained of the globular domain, F1-ATPase. They diffract to a resolution of 3-4 A and data collection is in progress. As a preliminary step towards crystallization of the entire complex, we have purified it from bovine mitochondria and reconstituted it into phospholipid vesicles.

Amino Acid Sequence↗

Analysis of Marek's disease virus serotype 1-specific phosphorylated polypeptides in virus-infected cells and Marek's disease lymphoblastoid cells.

By use of monoclonal antibodies, a virus-specific cytoplasmic antigen related to phosphorylated polypeptides specific to serotype 1 of Marek's disease virus (MDV)-related viruses (MDV1) has been identified in all MD tumour cell lines examined, as well as in infected cells and in tumour lesions of chickens with MD. At least two phosphorylated polypeptides with mol. wt. 39,000 (39K) to 36K and 24K (pp39/36 and pp24, respectively) were identified in the MD tumour cell line H10 cultured at 33 degrees C by immunoprecipitation with monoclonal antibody M21 which reacts with virus-specific phosphorylated polypeptides. These polypeptides were not detected in cells infected with MDV-related viruses of serotype 2 or 3. Immunoblot analysis indicated that these two polypeptides contained a serotype 1-specific epitope recognized with M21. An additional 41K polypeptide appeared in different virus strains of serotype 1. These polypeptides were found to contain phosphorylated serine but no detectable phosphorylated tyrosine or phosphorylated threonine. Cell fractionation indicated that the two phosphorylated polypeptides were mainly associated with smooth and rough endoplasmic reticulum fractions of cells infected with MDV1. Furthermore, the mRNA coding for pp39/36 could be separated from that coding for pp24 on a sucrose density gradient. These results suggest that pp24 and pp39/36 are translated from distinct mRNAs and encoded from overlapping genes or separate regions with partial DNA homology in the MDV1 genome.

Animals↗

The terminal protein gene 2 of Epstein-Barr virus is transcribed from a bidirectional latent promoter region.

The intact terminal protein genes (TP1 and TP2) of Epstein-Barr virus (EBV) are created upon infection by circularization of the linear viral genome at its terminal repeats. The structure of the 1.7 kb TP2 latent mRNA has been determined by cDNA analysis and Northern blotting, revealing its close relation to TP1 mRNA. The 1.7 kb transcript is expressed from a different promoter and has a different 5' exon from TP1 but is also spliced across the terminal repeats. The last eight exons are common to the TP1 and TP2 RNAs. The TP2 promoter is 3.3 kb downstream of the TP1 promoter and is part of a bidirectional latent EBV promoter region transcribing the TP2 and the latent membrane protein RNAs in opposite directions.

Cloning, Molecular↗

Efficient infection from cDNA clones of cucumber mosaic cucumovirus RNAs in a new plasmid vector.

Full-length cucumber mosaic cucumovirus (CMV) cDNAs were cloned into a new plasmid vector containing a modified plant virus promoter designed to transcribe the inserted sequence from its first nucleotide. cDNA copies of CMV strain Q (Q-CMV) genomic RNAs 1, 2 and 3 cloned into this vector were infectious when inoculated together, producing symptoms indistinguishable from those caused by wildtype Q-CMV infection. The infectivity of the clones could be substantially increased by excision of the viral insert together with the transcriptional promoter and terminator prior to inoculation. A diagnostic but silent mutation was introduced into the RNA 2 cDNA and found to be stably maintained in viral infection, allowing distinction of the recombinant virus from native contaminants. The infectious cDNA clones supported the replication of CMV satellite RNA when co-inoculated with biologically active Q-CMV satellite RNA transcripts. Using the infectious cDNAs described, it was found that a newly-identified overlapping gene (2b) encoded by Q-CMV RNA 2 was not essential for either systemic viral infection of Nicotiana glutinosa or replication of the satellite RNAs.

Base Sequence↗

The 25 amino acid residues at the carboxy terminus of the herpes simplex virus type 1 UL26.5 protein are required for the formation of the capsid shell around the scaffold.

Herpes simplex virus type 1 (HSV-1) polypeptides specified by overlapping genes UL26 and UL26.5 form a scaffold around which the icosahedral capsid shell is assembled. In a series of cleavage events catalysed by the UL26-encoded protease, the full-length UL26 product is processed into capsid proteins VP24 and VP21 and the UL26.5 protein is converted into the capsid protein VP22a by the loss of 25 amino acids from its carboxy terminus. The roles of the UL26 and UL26.5 products were investigated using the baculovirus expression system, focusing on the function of the 25 residues cleaved from the UL26.5 protein. A key conclusion from electron microscopic analysis and protein expression studies is that the 25 amino acids at the carboxy terminus of the full-length UL26.5 protein are required for the interaction of the capsid shell proteins with the scaffold in the formation of intermediate capsids. When cells were multiply infected with baculoviruses expressing a truncated form of the UL26.5 product corresponding to VP22a and the essential components of the capsid shell, no capsids were detected, whereas large numbers of capsids were observed when the full-length UL26.5 product was used as a scaffold. The results are consistent with the proposal that cleavage of the UL26.5 product occurs after capsid assembly or when the UL26.5 protein is in a complex with one or more capsid shell proteins. Expression of VP22a in the absence or presence of capsid shell proteins resulted in the formation of large numbers of 60 nm scaffold-like particles. Since VP22a expressed from baculovirus was unable to participate in capsid assembly, these particles cannot be intermediates in the capsid assembly pathway but may be similar in structure to the protein cores present in HSV-1 immature (B) capsids.

Amino Acid Sequence↗

Genetic analysis of full-length genomes and subgenomic sequences of TT virus-like mini virus human isolates.

The phylogenetic relationship between the complete genomic sequences of ten Japanese and one French isolate of TT virus-like mini virus (TLMV) was investigated. Analysis of the variability of the nucleotide sequences and the detection of signature patterns for overlapping genes suggested that ORFs 1 and 2 are probably functional. However, this was not the case for a putative third ORF, ORF3. Throughout the viral genome, several nucleotide or amino acid motifs that are conserved in circoviruses such as TT virus (TTV) and chicken anaemia virus were identified. Phylogenetic analysis distinguished three main groups of TLMV and allowed the identification of putative recombination breakpoints in the untranslated region. TLMV genomes were detected by PCR in the plasma of 38/50 French blood donors tested and were also identified in peripheral blood mononuclear cells, faeces and saliva. A phylogenetic study of 37 TLMV strains originating from France, Japan and Brazil showed that groupings were not related to geographical origin.

Base Composition↗

Complementation of daptomycin dptA and dptD deletion mutations in trans and production of hybrid lipopeptide antibiotics.

Daptomycin is a lipopeptide antibiotic produced by Streptomyces roseosporus and recently commercialized as Cubicin (daptomycin-for-injection) for treatment of skin and skin-structure infections caused by Gram-positive pathogens. Daptomycin is synthesized by a non-ribosomal peptide synthetase (NRPS) encoded by three overlapping genes, dptA, dptBC and dptD. The dptE and dptF genes, immediately upstream of dptA, are likely to be involved in the initiation of daptomycin biosynthesis by coupling decanoic acid to the N-terminal Trp. Analysis of RT-PCR data suggests that dptE, dptF, dptA, dptBC, dptD and possibly other dpt genes are transcribed as one large message; however, it has been demonstrated that sequential translation of these genes from a long transcript is not essential for robust daptomycin production. The dptA and the dptD genes were deleted from the dpt gene cluster, and expressed from ectopic positions in the chromosome under the control of the strong constitutive ermEp* promoter to produce high levels of lipopeptides. This three-locus trans-complementation system was used to produce hybrid lipopeptide antibiotics by introducing the heterologous lptD and cdaPS3 genes from Streptomyces fradiae and Streptomyces coelicolor, respectively, to complement the DeltadptD mutation.

Anti-Bacterial Agents↗

The heme-oxygenase family required for phytochrome chromophore biosynthesis is necessary for proper photomorphogenesis in higher plants.

The committed step in the biosynthesis of the phytochrome chromophore phytochromobilin involves the oxidative cleavage of heme by a heme oxygenase (HO) to form biliverdin IXalpha. Through positional cloning of the photomorphogenic mutant hy1, the Arabidopsis HO (designated AtHO1) responsible for much of phytochromobilin synthesis recently was identified. Using the AtHO1 sequence, we identified families of HO genes in a number of plants that cluster into two subfamilies (HO1- and HO2-like). The tomato (Lycopersicon esculentum) yg-2 and Nicotiana plumbaginifolia pew1 photomorphogenic mutants are defective in specific HO genes. Phenotypic analysis of a T-DNA insertion mutant of Arabidopsis HO2 revealed that the second HO subfamily also contributes to phytochromobilin synthesis. Homozygous ho2-1 plants show decreased chlorophyll accumulation, reduced growth rate, accelerated flowering time, and reduced de-etiolation. A mixture of apo- and holo-phyA was detected in etiolated ho2-1 seedlings, suggesting that phytochromobilin is limiting in this mutant, even in the presence of functional AtHO1. The patterns of Arabidopsis HO1 and HO2 expression suggest that the products of both genes overlap temporally and spatially. Taken together, the family of HOs is important for phytochrome-mediated development in a number of plants and that each family member may uniquely contribute to the phytochromobilin pool needed to assemble holo-phytochromes.

Amino Acid Sequence↗

Molecular mechanisms underlying the differential expression of maize pyruvate, orthophosphate dikinase genes.

I describe here the organization of maize C4 chloroplast and non-C4 cytosolic pyruvate, orthophosphate dikinase (PPDK) genes and the molecular mechanisms underlying their differential expression. The maize C4 chloroplast PPDK gene (C4ppdkZm1) appears to have been created by the addition of an exon encoding the chloroplast transit peptide at a site upstream of a cytosolic PPDK gene (cyppdkZm1). A splice acceptor sequence located in the first exon of cyppdkZm1 allows the fusion of the transit peptide to the cyppdkZm1 sequences. A second cyPPDK gene (cyppdkZm2) shares extensive homology with cyppdkZm1 in the coding region and in the 5' flanking region up to the TATA box. By a novel protoplast transient expression method, I show that the light-inducible expression of C4ppdkZm1 is controlled by two expression programs mediated through separate upstream regulatory elements that are active in leaf, but inactive in root and stem. Light-mediated C4ppdkZm1 expression in maize is apparently uncoupled from leaf development and partially associated with chloroplast development. For cyppdkZm1 expression, distinct upstream elements and a specific TATA promoter element, located in the first intron of C4ppdkZm1, are required. The low expression of cyppdkZm2 can be attributed to an absence of upstream positive elements and weak activity of the TATA promoter element.

Amino Acid Sequence↗