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At least 685 records · Page 38Linked to original sources
PubMed2002

Evolution of bacteriophage in continuous culture: a model system to test antiviral gene therapies for the emergence of phage escape mutants.

The emergence of viral escape mutants is usually a highly undesirable phenomenon. This phenomenon is frequently observed in antiviral drug applications for the treatment of viral infections and can undermine long-term therapeutic success. Here, we propose a strategy for evaluating a given antiviral approach in terms of its potential to provoke the appearance of resistant virus mutants. By use of Q beta RNA phage as a model system, the effect of an antiviral gene therapy, i.e., a virus-specific repressor protein expressed by a recombinant Escherichia coli host, was studied over the course of more than 100 generations. In 13 experiments carried out in parallel, 12 phage populations became resistant and 1 became extinct. Sequence analysis revealed that only two distinct phage mutants emerged in the 12 surviving phage populations. For both escape mutants, sequence variations located in the repressor binding site of the viral genomic RNA, which decrease affinity for the repressor protein, conferred resistance to translational repression. The results clearly suggest the feasibility of the proposed strategy for the evaluation of antiviral approaches in terms of their potential to allow resistant mutants to appear. In addition, the strategy proved to be a valuable tool for observing virus-specific molecular targets under the impact of antiviral drugs.

Allolevivirus↗
PubMed1992

The origin and early evolution of nucleic acid polymerases.

The hypothesis that vestiges of the ancestral RNA-dependent RNA polymerase involved in the replication of RNA genomes of Archean cells are present in the eubacterial RNA polymerase beta' subunit and its homologues is discussed. We show that in the DNA-dependent RNA polymerases from the three cellular lineages a very conserved sequence of eight amino acids also found in a small RNA-binding site previously described for the E. coli polynucleotide phosphorylase and the S1 ribosomal protein is present. The optimal conditions for the replicase activity of the avian myeloblastosis virus reverse transcriptase are presented. The evolutionary significance of the in vitro modifications of substrate and template specificities of RNA polymerases and reverse transcriptases is also discussed.

Amino Acid Sequence↗
PubMed2000

Sequences of Citrus tristeza virus separated in time and space are essentially identical.

The first Citrus tristeza virus (CTV) genomes completely sequenced (19.3-kb positive-sense RNA), from four biologically distinct isolates, are unexpectedly divergent in nucleotide sequence (up to 60% divergence). Understanding of whether these large sequence differences resulted from recent evolution is important for the design of disease management strategies, particularly the use of genetically engineered mild (essentially symptomless)-strain cross protection and RNA-mediated transgenic resistance. The complete sequence of a mild isolate (T30) which has been endemic in Florida for about a century was found to be nearly identical to the genomic sequence of a mild isolate (T385) from Spain. Moreover, samples of sequences of other isolates from distinct geographic locations, maintained in different citrus hosts and also separated in time (B252 from Taiwan, B272 from Colombia, and B354 from California), were nearly identical to the T30 sequence. The sequence differences between these isolates were within or near the range of variability of the T30 population. A possible explanation for these results is that the parents of isolates T30, T385, B252, B272, and B354 have a common origin, probably Asia, and have changed little since they were dispersed throughout the world by the movement of citrus. Considering that the nucleotide divergence among the other known CTV genomes is much greater than those expected for strains of the same virus, the remarkable similarity of these five isolates indicates a high degree of evolutionary stasis in some CTV populations.

Base Sequence↗
PubMed2001

Sequence comparison and phylogenetic analysis of fish nodaviruses based on the coat protein gene.

We have amplified by reverse transcription-polymerase chain reaction (RT-PCR) and sequenced a 605-bp fragment covering the variable region of the coat protein gene of fish nodaviruses infecting European sea bass, Dicentrarchus labrax (n = 24), and shi drum, Umbrina cirrosa (n = 2), in the Mediterranean basin. Nine new isolates were identified and their sequences were combined with sequences in the literature to produce three different data sets. The first set, based on amino acid sequences, was used to verify the monophyly of fish nodaviruses. The second and third data sets, based on nucleic acids, were used to resolve the phylogenetic relationships between closely related fish nodaviruses. Phylogenetic analyses were performed according to the maximum parsimony and neighbor-joining methods. Our results support the monophyly of fish nodaviruses. Moreover, they confirm the subdivision of fish nodaviruses into four main clusters, in agreement with the previously suggested phylogeny of the genus Piscinodavirus, that was based on a smaller number of sequences and an alternative phylogenetic approach [14]. All the Mediterranean isolates were clustered in the group of the red-spotted grouper nervous necrosis virus and appear to have a restricted geographic distribution, except for one sequence-type (10 samples) that is widespread throughout the basin.

Animals↗
PubMed1996

cis-acting elements within an RNA coliphage genome: fold as you please, but fold you must!!

Using an in vivo complementation system, we conducted a mutational analysis of the bacteriophage Q beta readthrough cistron. In the Q beta cDNA-containing plasmid, pQ beta m100, we constructed six defined Q beta deletion cDNA genomes, each missing between 86 and 447 nucleotides from within the readthrough cistron. These deletion plasmids were introduced into host cells that are constitutively supplied with Q beta readthrough protein from the plasmid pQ beta RT. Under these conditions, all six deletion genomes spontaneously generated phage particles, each exhibiting a characteristic plaque phenotype and virus forming potential. Isolated readthrough-defective phage particles were subsequently used to infect host cells that carried helper readthrough protein. Passaged viruses yielded both larger plaques and higher titers, compared with those of the parent phages. Sequence analysis revealed that the genomes of the passaged viruses had deleted additional regions of readthrough RNA sequence. We discuss the possibilities that (1) the disruption of a well-defined structural domain in Q beta RNA was selectively disadvantageous to phage infection, and that (2) the evolved viral populations were selected by virtue of their ability to restore critical integrity of short and/or long-range nucleotide interactions within this region of Q beta RNA.

Base Sequence↗
PubMed2001

A selection system for identifying accessible sites in target RNAs.

Although ribozymes offer tremendous potential for posttranscriptionally controlling expression of targeted genes, their utility is often limited by the accessibility of the targeted regions within the RNA transcripts. Here we describe a method that identifies RNA regions that are accessible to oligonucleotides. Based on this selection protocol, we show that construction of hammerhead ribozymes targeted to the identified regions results in catalytic activities that are consistently and substantially greater than those of ribozymes designed on the basis of computer modeling. Identification of accessible sites should also be widely applicable to design of antisense oligonucleotides and DNAzymes.

Base Sequence↗
PubMed2000

Sugarcane yellow leaf virus: an emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors.

We have derived the genomic nucleotide sequence of an emerging virus, the Sugarcane yellow leaf virus (ScYLV), and shown that it produces one to two subgenomic RNAs. The family Luteoviridae currently includes the Luteovirus, Polerovirus, and Enamovirus genera. With the new ScYLV nucleotide sequence and existing Luteoviridae sequence information, we have utilized new phylogenetic and evolutionary methodologies to identify homologous regions of Luteoviridae genomes, which have statistically significant altered nucleotide substitution ratios and have produced a reconstructed phylogeny of the Luteoviridae. The data indicate that Pea enation mosaic virus-1 (PEMV-1), Soybean dwarf virus (SbDV), and ScYLV exhibit spatial phylogenetic variation (SPV) consistent with recombination events that have occurred between poleroviral and luteoviral ancestors, after the divergence of these two progenitor groups. The reconstructed phylogeny confirms a contention that a continuum in the derived sequence evolution of the Luteoviridae has been established by intrafamilial as well as extrafamilial RNA recombination and expands the database of recombinant Luteoviridae genomes that are currently needed to resolve better defined means for generic discrimination in the Luteoviridae (D'Arcy, C. J. and Mayo, M. 1997. Arch. Virol. 142, 1285-1287). The analyses of the nucleotide substitution ratios from a nucleotide alignment of Luteoviridae genomes substantiates the hypothesis that hot spots for RNA recombination in this virus family are associated with the known sites for the transcription of subgenomic RNAs (Miller et al. 1995. Crit. Rev. Plant Sci. 14, 179-211), and provides new information that might be utilized to better design more effective means to generate transgene-mediated host resistance.

Amino Acid Sequence↗
PubMed2005

Molecular characterization of the HA gene of influenza type B viruses.

Nucleotide sequences of the HA1 subunit of influenza B viruses isolated in Portugal between 1994 and 2003 influenza winter seasons were analyzed by the Neighbor-Joining algorithm and rates of HA1 evolution estimated by linear regression. From 1994 to 2002, all influenza B viruses studied were of the Yamagata lineage. Strains isolated from 1994 to 1996, 1996 to 1999, and 1999 to 2002 revealed a high similarity with B/Beijing/184/93, B/Yamanashi/166/98, and B/Sichuan/379/99, respectively, and strains isolated during 1994-1995, 1996-1997, and 1998-1999 clustered in more than one branch of the phylogenetic tree. Victoria-related strains reappeared during 2002/2003 and formed only one branch in the phylogenetic tree revealing a closer relationship to B/Shandong/7/97. Evolutionary rates for strains from the Yamagata lineage were estimated as 3.82x10(-3) nucleotides/site/year and 2.62x10(-3) nucleotides/site/year for Victoria-related strains. In order to identify putative influenza B HA1 codons under selective pressure, a codon-substitution model for heterogeneous selective pressure at amino acid sites was used. A percentage of 97.3% of codons under negative selective pressure and 2.7% of codons under positive selective pressure (omega=dN/dS=2.65) were estimated, with posterior probability higher than 0.90. Amino acid sites 75, 197, and 199 were found more likely to be under positive selective pressure.

Antigenic Variation↗
PubMed2000

Concurrent neutral evolution of mRNA secondary structures and encoded proteins.

Messenger RNA sequences often have to preserve functional secondary structure elements in addition to coding for proteins. We present a statistical analysis of retroviral mRNA which supports the hypothesis that the natural genetic code is adapted to such complementary coding. These sequences are still able to explore efficiently the space of possible proteins by point mutations. This is borne out by the observation that, in stem regions of retroviral mRNA foldings, silent mutations on one strand are preferentially accompanied by conservative mutations on the other. Distances between amino acids based on physicochemical properties are used to quantify the conservation of protein function under the constraint of maintained RNA secondary structure. We find that preservation of RNA secondary structure by compensatory mutations is evolutionary compatible with the efficient search for new variants on the protein level.

Base Sequence↗
PubMed2005

Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection.

Between 1996 and 1998, two clades (B and C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000, a third clade (A; genotype III) of DENV-1, which had been circulating at that locality for at least 25 years, became extinct. These changes preceded the largest outbreak of dengue recorded in Myanmar, in 2001, in which more than 95% of viruses recovered from patients were DENV-1, but where the incidence of severe disease was much less than in previous years. Phylogenetic analyses of viral genomes indicated that the two new clades of DENV-1 did not arise from the, now extinct, clade A viruses nor was the extinction of this clade due to differences in the fitness of the viral populations. Since the extinction occurred during an inter-epidemic period, we suggest that it was due to a stochastic event attributable to the low rate of virus transmission in this interval.

Aedes↗
PubMed1997

Evolution of bacterial genomes.

This review examines evolution of bacterial genomes with an emphasis on RNA based life, the transition to functional DNA and small evolving genomes (possible plasmids) that led to larger, functional bacterial genomes.

Bacteria↗
PubMed2001

Satsuma dwarf and related viruses belong to a new lineage of plant picorna-like viruses.

Satsuma dwarf virus (SDV) and two closely related viruses, Citrus mosaic (CiMV), and Naval orange infectious mottling (NIMV), seriously affect citrus varieties grown in Japan and East Asia. All three viruses have icosahedral particles built of two proteins encapsidating two single-stranded genomic RNAs. The natural mode of transmission of these SDV-like viruses is unknown, and they were previously placed among tentative members of the family Comoviridae. Recently, a complete genome of SDV was sequenced, and its replication-related proteins were found only distantly related to those of viruses from the family Comoviridae (Iwanami T., Kondo Y., and Karasev A.V. J Gen Virol 80, 793-797, 1999). Here we present a partial genome sequence for another SDV-like virus, NIMV, and a thorough phylogenetic analysis of the gene products encoded by SDV, CiMV, and NIMV to assess their relationships with picorna-like viruses infecting plants, insects, and vertebrates. The RdRp's of SDV-like viruses form a new lineage, separate from members of Como- and Sequiviridae families. Phylogenetic analysis suggests that SDV-like viruses may represent a new family of plant picorna-like viruses. Sequence analysis of the capsid proteins (CPs) encoded by the SDV-like viruses revealed a region of similarity to CPs of animal calici- and picornaviruses that encompasses the structural core of the eight-strand beta-barrel characteristic of picornaviral CPs. These data suggest that SDV and related bipartite viruses evolved separately from the viruses in the family Comoviridae and that the split of an ancestor, monopartite picorna-like virus genome might have occurred more than once.

Amino Acid Sequence↗