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At least 1,135 records · Page 63Linked to original sources
PubMed2006

A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes.

Genomic analysis of bacteriophages frequently reveals a mosaic structure made up from modules that come from disparate sources. This fact has led to the general acceptance of the notion that rampant and promiscuous lateral gene transfer (LGT) plays a critical role in phage evolution. However, recent sequencing of a series of the T4-type phages has revealed that these large and complex genomes all share 2 substantial syntenous blocks of genes encoding the replication and virion structural genes. To analyze the pattern of inheritance of this core T4 genome, we compared the complete genome sequences of 16 T4-type phages. We identified a set of 24 genes present in all these T4-type genomes. Somewhat surprisingly, only one of these genes, that encodes for ribonucleotide reductase (NrdA), displayed evidence of LGT with the bacterial host. We test the congruence of the inheritance of the other 23 markers using heat map analyses and comparison of a reference topology with the 23 individual gene phylogenies. The vast majority of these core genes share a common evolutionary history. In contrast, analyses of all the noncore genes present in the same 16 genomes, located in the hyperplastic regions of the genome, show considerable evidence of frequent LGT. The similar evolution of the core replication and virion structural genes in the T4-type phage genomes suggests that, unlike the situation in many other phage groups, such portions of T4-type genome have been inherited as a block, without significant LGT, from a distant common ancestor. The preservation of the synteny of the core T4 genome could result from several factors acting in synergy, such as the constraints imposed by the sophisticated regulation of the transcription. Moreover, numerous and complex protein-protein interactions during virion morphogenesis could also impose a supplementary barrier against LGT. Finally, there may be some real evolutionary advantage to maintaining large regions of conserved sequence. Such segments could be a sort of genetic glue that maintains the genetic cohesion of the T4-type phages via recombination within the most conserved sequences. This could mediate the swapping of nonconserved sequences that they flank.

Bacteriophage T4↗
PubMed1996

Identification of two separate domains in the influenza virus PB1 protein involved in the interaction with the PB2 and PA subunits: a model for the viral RNA polymerase structure.

The domains of the PB1 subunit of the influenza virus polymerase involved in the interaction with the PB2 and PA subunits have been defined by mutational analysis of PB1 protein. The experimental approach included in vivo competition of the PB1 activity, two-hybrid interaction assays and in vitro binding to PB1-specific matrices. Mutants of the PB1 gene including N-terminal, C-terminal and internal deletions and single amino acid insertions were constructed. They were unable to support polymerase activity in a reconstituted transcription-replication system and were tested for their competition activity when expressed in excess over wild-type PB1 protein. The pattern of competition obtained suggested that the N-terminal 78 amino acids and the sequences between positions 506 and 659 in the PB1 protein are involved in the interaction with the other components of the polymerase. We identified the N-terminal region of PB1 protein as responsible for the interaction with the PA subunit by two-hybrid assays in mammalian cells. N- and C-terminal fragments of the PB1 protein were expressed as His-tagged proteins and purified on Ni2+-NTA resin. Such PB1-specific matrices were used in binding assays in vitro with metabolically labelled PB2 and PA proteins and mutants thereof. The results obtained indicated that the N-terminal and the C-terminal regions of PB1 are responsible for binding to PA and PB2 subunits, respectively. With this information and previously published results we propose a preliminary model for the architecture of the influenza virus RNA polymerase.

Animals↗
PubMed2005

HLA-B27: portraying immunodominant viral epitopes.

Although the crystal structure of HLA-B27 has been known for a long time, only recently have X-ray diffraction studies of this molecule in complex with individual peptides become available. The report of three such structures involving viral epitopes that are immunodominant in HLA-B27-restricted T cell responses against influenza, Epstein-Barr and HIV viruses significantly improves our perception of critical aspects of the immunological and pathogenetic roles of HLA-B27, including (1) the molecular basis of its peptide-binding specificity and how this is modulated by subtype polymorphism, (2) the relationship between the structural and the antigenic features of immunodominant viral epitopes, (3) the basis for long term non-progression to AIDS of HIV-infected HLA-B27+ individuals, and (4) the structural features of microbial peptides influencing NK receptor engagement. Here, I discuss the implications of this and related studies for the relevance of HLA-B27 in host defense and as a pathogenetic molecule in spondyloarthritis.

Antigens, Viral↗
PubMed1984

A second cauliflower mosaic virus gene product influences the structure of the viral inclusion body.

We have used electron microscopy of thin sections and experiments on isolated viroplasms to compare the properties of four strains of cauliflower mosaic virus (CaMV), three of which were partially or completely deleted in open reading frame (ORF) II. Our results confirm that this gene is required for aphid transmissibility and show that the product of ORF II influences the firmness with which virions are held within the viroplasm. Analysis of the proteins in the viroplasms showed that a mutant with a partial deletion in ORF II produced a protein smaller than the normal ORF product. This smaller protein was non-functional with respect both to aphid transmissibility and properties of the viroplasms.

Journal Article↗
PubMed1990

Identification and sequencing of the spheroidin gene of Choristoneura biennis entomopoxvirus.

Entomopoxviruses are a class of insect viruses whose virions are embedded in cytoplasmic occlusion bodies. The major component of these protective complexes is a protein called spheroidin. An open reading frame encoding the spheroidin gene of Choristoneura biennis entomopoxvirus has been identified and sequenced in our laboratory. This protein coding region is 1023 nucleotides long and specifies a polypeptide of 38,500 Da. Spheroidin was purified by SDS polyacrylamide gel electrophoresis, electroeluted, and its amino terminus sequence was determined on a gas phase sequencer. We observed that the first 20 N-terminal amino acids were absent in the mature processed form of the spheroidin molecule. Examination of these 20 residues revealed their hydrophobic nature and close resemblance to the consensus signal peptide sequence which is commonly found on membrane proteins. The DNA sequence of the spheroidin gene predicted a processed polypeptide with a molecular weight of 36 kDa. However, spheroidin was observed to aggregate in complexes composed of 50-kDa monomers. Intermolecular disulfide bonds were shown to play major roles in the formation and structure of these viral occlusion bodies. The difference in molecular weight between the predicted protein and its counterpart in infected cells is likely due to post-translational modifications. Indeed, two potential asparagine-linked glycosylation sites are present on the spheroidin molecule. The 5' flanking regions of the spheroidin gene and the vaccinia major core protein precursor gene P4b were shown to share substantial homology.

Amino Acid Sequence↗
PubMed1998

Structural characterization of viral neutralizing monoclonal antibodies to hepatitis B surface antigen.

In this study we describe the viral neutralizing activity of murine monoclonal antibodies (MAb) specific for hepatitis B surface antigen (HBsAg). This viral neutralizing activity was assessed in vitro by employing Hepatitis Delta Virus (HDV) and human hepatocytes as target cells. To further characterize these viral neutralizing antibodies we generated a panel of anti-idiotypic (anti-Id) reagents and serologically characterized these antibodies for epitope specificity, Id specificity, and Id heterogeneity. Direct binding and competitive inhibition solid phase enzyme immunoassay have demonstrated that two murine MAb specific for HBsAg (anti-HBs), designated A1.2 and A3.1, recognize similar or overlapping epitopes on HBsAg, while monoclonal anti-HBs, designated A2.1 recognizes a unique HBsAg epitope. Further, Id analysis using monoclonal and polyclonal anti-Id reagents have identified both a private and a cross-reactive Id, respectively, on the anti-HBs, A1.2 preparation. The source of the idiotypic cross-reactivity between A1.2 and A3.1 has been identified, using Western blot analysis, to conformational determinants expressed by the heavy (H) and light (L) chains of these monoclonal anti-HBs. Lastly, the intrastrain antibody repertoire induced following HBsAg immunization was found to be relatively restricted in heterogeneity by clonotype analysis using isoelectric focusing and affinity immunoblot analysis. Interspecies variability in the anti-HBs response was observed based on epitope recognition using purified anti-HBs from a variety of species.

Animals↗