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PubMed1982

Evidence for an early evolutionary origin and locus polymorphism of mouse VL30 DNA sequences.

The VL30 sequences of mouse DNA are a family of sequences with retrovirus-like structure which code for a 30S RNA transcript that can be packaged into the virions of murine leukemia viruses and thereby transmitted from cell to cell. A Southern blot analysis of these sequences revealed that multiple copies are present in the DNA of all mice examined, regardless of species or geographic origin. Considerable locus polymorphism was also apparent, and at least one of these polymorphisms appeared to reflect the differing chromosomal location of a complete VL30 sequence. These data indicated that VL30 elements are not recent additions to the mouse genome and suggested that the evolution of the VL30 multigene family has been accompanied by duplication and dispersion of VL30 sequences to diverse genomic sites. In addition, we reexamined the issue of genetic relatedness between mouse VL30 sequences and a physically similar family of virus-like elements in the rat genome. We found that many, if not all, rat and mouse VL30 loci contain regions of sequence homology. These data suggested that rodent VL30 sequences have evolved from a common ancestral sequence.

Animals↗
PubMed2002

Comparative rates of nucleotide sequence variation in the hypervariable region of E1/E2 and the NS5b region of hepatitis C virus in patients with a spectrum of liver disease resulting from a common source of infection.

The association of the severity of liver disease and the molecular evolution of hepatitis C virus (HCV) during chronic infection remains unclear and controversial. To address this we have studied the interpatient variability in the nucleotide sequence of two regions of the HCV genome, E1/E2, which contain the hypervariable region 1 and the nonstructural NS5b region, in a cohort of Irish female patients who were all recipients of a single source of HCV genotype 1b-contaminated anti-D immunoglobulin in 1977 and 1978 and who over the subsequent 20 years developed a spectrum of liver disease. In addition, quasispecies analysis was used to evaluate intrapatient variability in the E1/E2 region in four patients with mild and four with severe disease. Phylogenetic and evolutionary rate analyses of the nucleotide sequences demonstrated that there was no significant difference between those who developed mild disease and those who had progressed to severe disease or cirrhosis. These findings suggest that other factors, either additional viral or host, may be important in the pathogenesis and clinical outcome of chronic hepatitis C virus infection.

Amino Acid Sequence↗
PubMed2005

Population structure within lineages of Wheat streak mosaic virus derived from a common founding event exhibits stochastic variation inconsistent with the deterministic quasi-species model.

Structure of Wheat streak mosaic virus (WSMV) populations derived from a common founding event and subjected to serial passage at high multiplicity of infection (MOI) was evaluated. The founding population was generated by limiting dilution inoculation. Lineages of known pedigree were sampled at passage 9 (two populations) and at passage 15, with (three populations) or without mixing (four populations) of lineages at passage 10. Polymorphism within each population was assessed by sequencing 17-21 clones containing a 1371 nt region (WSMV-Sidney 81 nts 8001-9371) encompassing the entire coat protein cistron and flanking regions. Mutation frequency averaged approximately 5.0 x 10(-4)/nt across all populations and ranged from 2.4 to 11.6 x 10(-4)/nt within populations, but did not consistently increase or decrease with the number of passages removed from the founding population. Shared substitutions (19 nonsynonymous, 10 synonymous, and 3 noncoding) occurred at 32 sites among 44 haplotypes. Only four substitutions became fixed (frequency = 100%) within a population and nearly one third (10/32) never achieved a frequency of 10% or greater in any sampled population. Shared substitutions were randomly distributed with respect to genome position, with transitions outnumbering transversions 5.4:1 and a clear bias for A to G and U to C substitutions. Haplotype composition of each population was unique with complexity of each population varying unpredictably, in that the number and frequency of haplotypes within a lineage were not correlated with number of passages removed from the founding population or whether the population was derived from a single or mixed lineage. The simplest explanation is that plant virus lineages, even those propagated at high MOI, are subject to frequent, narrow genetic bottlenecks during systemic movement that result in low effective population size and stochastic changes in population structure upon serial passage.

Base Sequence↗
PubMed1999

Update on prevention and treatment of viral hepatitis in children.

Viral hepatitis is a persisting concern. Outbreaks of hepatitis A occur in developed countries where only 10% to 20% of the population is seroprotected. The disease may cause fulminant liver failure and death. People who are targeted for vaccination include intravenous drug users, homosexuals, and chronic hepatitis patients. Secondary prophylaxis of household contacts is an efficient way to prevent secondary cases. Universal vaccination is now in progress for hepatitis B. Vaccination failure may occur in low birth weight infants, or in infants infected in utero. Chronic carriers of viral hepatitis may progress to cirrhosis and hepatocarcinoma, the latter risk being most important for men infected at birth. Alcohol intake should be avoided in carrier adolescents. Interferon is able to triple the rate of hepatitis B e antigen loss and decouple the rate of hepatitis B s antigen loss after one year, shortening disease evolution and, it is to be hoped, decreasing the risk of unfavorable outcome. Similarly, lamivudine increases by four times the rate of hepatitis B e antigen loss in adults. However, precore mutants may be selected by immune pressure after seroconversion in children, and tyrosine-methionine-aspartate-aspartate (YMDD) mutations appear in 15% of patients treated with lamivudine after 1 year. Hepatitis C is mainly acquired during childhood via true vertical transmission. The risk of acquiring Hepatitis C is related to the presence and amount of RNA for hepatitis C virus in mothers at the time of birth. The infection rate for the hepatitis C virus is higher in children from mothers who have tested positive for HIV, and higher if these children are themselves coinfected with HIV. Treatment with interferon alone has a poor rate of efficiency, although pediatric studies remain scarce. Combination treatment using ribavirin plus interferon yield a higher rate of success in eradicating viral infection in adults.

Child↗
PubMed1995

Complete nucleotide sequence of RNA segment 3 of bluetongue virus serotype 2 (Ona-A). Phylogenetic analyses reveal the probable origin and relationship with other orbiviruses.

The nucleotide sequence of the RNA segment 3 of bluetongue virus (BTV) serotype 2 (Ona-A) from North America was determined to be 2772 nucleotides containing a single large open reading frame of 2703 nucleotides (901 amino acid). The predicted VP3 protein exhibited general physiochemical properties (including hydropathy profiles) which were very similar to those previously deduced for other BTV VP3 proteins. Partial genome segment 3 sequences, obtained by polymerase chain reaction (PCR) sequencing, of BTV isolates from the Caribbean were compared to those from North America, South Africa, India, Indonesia, Malaysia and Australia, as well as other orbiviruses, to determine the phylogenetic relationships amongst them. Three major BTV topotypes (Gould, A.R. (1987) Virus Res. 7, 169-183) were observed which had nucleotide sequences that differed by approximately 20%. At the molecular level, geographic separation had resulted in significant divergence in the BTV genome segment 3 sequences, consistent with the evolution of distinct viral populations. The close phylogenetic relationship between the BTV serotype 2 (Ona-A strain) from Florida and the BTV serotypes 1, 6 and 12 from Jamaica and Honduras, indicated that the presence of BTV serotype 2 in North America was probably due to an exotic incursion from the Caribbean region as previously proposed by Sellers and Maaroof ((1989) Can. J. Vet. Res. 53, 100-102) based on trajectory analysis. Conversely, nucleotide sequence analysis of Caribbean BTV serotype 17 isolates suggested they arose from incursions which originated in the USA, possibly from a BTV population distinct from those circulating in Wyoming.

Amino Acid Sequence↗
PubMed1997

Coat protein gene and 3'-noncoding region of a new Korean isolate of cymbidium mosaic virus.

A new Korean isolate of cymbidium mosaic virus (denoted as CymMV-K2), a member of potexviruses, was identified and isolated from a Korean cultivar of Cymbidium species When the nucleotide sequence of the 3'-terminal region of the viral RNA was compared with those of the corresponding regions of two Singaporean isolates (denoted as CymMV-S1 and CymMV-S2) and a Korean isolate (denoted as CymMV-K1), the nucleotide sequence of the coat protein gene of CymMV-K2 was highly homologous to other cymbidium mozaic viruses (92.9%-96.7% homology). The coat protein of CymMV-K2 and CymMV-S2 consists of 223 amino acids, while the coat protein of CymMV-K1 and CymMV-S1 consists of 220 amino acids. This difference was caused by deletions of 5 nucleotides in the coat protein open reading frame (ORF) of CymMV-S1 and CymMV-K1, when compared with CymMV-K2 and CymMV-S2. These deletions result in changes of the deduced amino acid sequence and the length of the coat protein. The 3'-noncoding region of the CymMV-K2, which contains sequences involved in the replication and polyadenylation of viral RNA, was compared with those of other cymbidium mosaic viruses. No canonical polyadenylation signal was found in the 3'-noncoding region of CymMV-K2, whereas in other CymMVs AAUAAA boxes, are present at the end of RNA with their AAA portions as the first A residue of the poly(A) tail.

Amino Acid Sequence↗
PubMedDate not supplied

Structure of a human common cold virus and functional relationship to other picornaviruses.

We report the first atomic resolution structure of an animal virus, human rhinovirus 14. It is strikingly similar to known icosahedral plant RNA viruses. Four neutralizing immunogenic regions have been identified. These, and corresponding antigenic sequences of polio and foot-and-mouth disease viruses, reside on external protrusions. A large cleft on each icosahedral face is probably the host cell receptor binding site.

Amino Acids↗
PubMed1975

Endogenous primate and feline type C viruses.

1. Endogenous type C viruses have been detected in a wide variety of mammalian species. Multiple copies of related, but not identical, virogene sequences can be found in the DNA of these species. 2. The endogenous type C virogenes are subject to the pressures of natural selection, and closely related species possess related virogene sequences. These genes evolve as cellular entities diverging from one another in a manner which correlates well with taxonomic relatedness of the species. 3. The endogenous type C viruses of baboons and domestic cats are related, but they can be distinguished by biologic and immunologic criteria and by partial nucleic acid sequence homology. Virogene sequences in the DNA of Old World monkeys and domestic cats also show a degree of relatedness not shared by the unique sequence DNA of these species. The data suggest that progenitors of domestic cats were exogenously infected by a type C virus that also gave rise to present-day endogenous type C viruses of Old World monkeys. 4. The genomes of exogenously infectious viruses replicating in permissive host cells appear to evolve much more rapidly than endogenous virogenes which replicate as cellular genes. Laboratory strains of efficiently oncogenic type C viruses are presumed to be derived from activated endogenous viruses which have been selected for virulence and which, in certain cases, have acquired the capacity to replicate in the host's own cells. 5. The ubiquitous presence of endogenous type C viruses among vertegrates and their preservation throughout millions of years of evolution suggests that these genes express normal physiologic functions which provide a selective advantage to the species.

Animals↗
PubMed2005

[Molecular epidemiology of Xinjiang hemorrhagic fever viruses].

BACKGROUND: To study the molecular biology of Xinjiang hemorrhagic fever (XHF) viruses, to explore its relationship with other Crimean-Congo hemorrhagic fever viruses, analyzing the epidemic origin and the tendency of geographic distribution of XHF. METHODS: The S partial segment from the patient and tick samples collected in 2001 and 2002 was tested by RT-PCR, the positive samples were sequenced directly. The nucleotide homology of S partial segment as well as the whole segments were analyzed and the phylogenetic tree of S and M gene segments was drawn by computer. RESULTS: All compared sequences of S partial segments from the patient and tick samples showed a high homology of nucleotide sequences. Phylogenetic tree divided all the analyzed viruses into three groups; Europe, African and Asian group. The Asian group can be divided further into another two branches: the middle Asian branch and the Chinese branch. All the Chinese isolates were clustered into one single group and was easy to be discriminated from the other isolates. The dividing of M segments seemed not completely related to the geographic origin of the viruses. CONCLUSION: M segment classification was not consistent to the geographic distribution of the viruses. S segments analysis showed the close relationship of genetic background between the patient isolates and the tick isolates. Besides, all the Chinese isolates have the common evolution route and the gene structure characteristics displayed the regional distribution pattern.

Animals↗
PubMed2003

Fitness of a turnip crinkle virus satellite RNA correlates with a sequence-nonspecific hairpin and flanking sequences that enhance replication and repress the accumulation of virions.

satC, a satellite RNA associated with Turnip crinkle virus (TCV), enhances the ability of the virus to colonize plants by interfering with stable virion accumulation (F. Zhang and A. E. Simon, unpublished data). Previous results suggested that the motif1-hairpin (M1H), a replication enhancer on minus strands, forms a plus-strand hairpin flanked by CA-rich sequence that may be involved in enhancing systemic infection (G. Zhang and A. E. Simon, J. Mol. Biol. 326:35-48, 2003). In this study, sequence and structural requirements of the M1H were further assayed by replacing the 28-base M1H with 10 random bases and then subjecting the pool of satellite RNA to functional selection in plants. Unlike previous results with 28-base replacement sequences (G. Zhang and A. E. Simon, J. Mol. Biol. 326:35-48, 2003), only a few of the 10-base SELEX (systematic evolution of ligands by exponential enrichment) assay winners contained short motifs in their minus-sense orientation that were similar to TCV replication elements. However, all second- and third-round winning replacement sequences folded into hairpins flanked by CA-rich sequence predicted to be more stable on plus strands than minus strands. Plus strands of several of the most fit satellite RNAs contained insertions of CA-rich sequence at the base of their hairpins whose presence correlated with enhanced replication and reduced detection of virions. Deletion of the M1H resulted in no detectable virions despite very low satellite accumulation. These results support the hypothesis that a sequence-nonspecific plus-strand hairpin brings together flanking CA-rich sequences in the M1H region that confers fitness to satC by reducing the accumulation of stable virions.

Base Sequence↗
PubMed2001

The msDNAs of bacteria.

msDNAs are small, structurally unique satellite DNAs found in a number of Gram-negative bacteria. Composed of hundreds of copies of single-stranded DNA--hence the name multicopy single-stranded DNA--msDNA is actually a complex of DNA, RNA, and probably protein. These peculiar molecules are synthesized by a reverse transcription mechanism catalyzed by a reverse transcriptase (RT) that is evolutionarily related to the polymerase found in the HIV virus. The genes, including the RT gene, responsible for the synthesis of msDNA are encoded in a retron, a genetic element that is carried on the bacterial chromosome. The retron is, in fact, the first such retroelement to be discovered in prokaryotic cells. This report is a comprehensive review of the many interesting questions raised by this unique DNA and the fascinating answers it has revealed. We have learned a great deal about the structure of msDNA: how it is synthesized, the structure and functions of the RT protein required to make it, its effects on the host cell, the retron element that encodes it, its possible origins and evolution, and even its potential usefulness as a practical genetic tool. Despite the impressive gains in our understanding of the msDNAs, however, the simple, fundamental question of its natural function remains an enduring mystery. Thus, we have much more to learn about the msDNAs of bacteria.

Bacteria↗
PubMed2003

Complete alanine scanning of intersubunit interfaces in a foot-and-mouth disease virus capsid reveals critical contributions of many side chains to particle stability and viral function.

Spherical virus capsids are large, multimeric protein shells whose assembly and stability depend on the establishment of multiple non-covalent interactions between many polypeptide subunits. In a foot-and-mouth disease virus capsid, 42 amino acid side chains per protomer are involved in noncovalent interactions between pentameric subunits that function as assembly/disassembly intermediates. We have individually truncated to alanine these 42 side chains and assessed their relevance for completion of the virus life cycle and capsid stability. Most mutations provoked a drastic reduction in virus yields. Nearly all of these critical mutations led to virions whose thermal inactivation rates differed from that of the parent virus, and many affected also early steps in the viral cycle. Rapid selection of genotypic revertants or variants with forward or compensatory mutations that restored viability was occasionally detected. The results with this model virus indicate the following. (i). Most of the residues at the interfaces between capsid subunits are critically important for viral function, in part but not exclusively because of their involvement in intersubunit recognition. Each hydrogen bond and salt bridge buried at the subunit interfaces may be important for capsid stability. (ii). New mutations able to restore viability may arise frequently at the subunit interfaces during virus evolution. (iii). A few interfacial side chains are functionally tolerant to truncation and may provide adequate mutation sites for the engineering of a thermostable capsid, potentially useful as an improved vaccine.

Alanine↗
PubMed1993

The type 1 human immunodeficiency virus Tat binding protein is a transcriptional activator belonging to an additional family of evolutionarily conserved genes.

The type 1 human immunodeficiency virus Tat protein is a powerful transcriptional activator when bound to an RNA structure (TAR) present at the extreme 5' terminus of viral mRNA. Since transcriptional activation requires binding of Tat to RNA, it has been suggested that Tat enhances initiation or elongation through a direct interaction with cellular transcription factors. Here we show through protein fusion experiments that the previously identified cellular Tat binding protein, TBP-1, although unable to bind DNA, is a strong transcriptional activator when brought into proximity of several promoter elements. Transcriptional activity depends upon the integrity of at least two highly conserved domains: one resembling a nucleotide-binding motif and the other motif common to proteins with helicase activity. Our studies further reveal that TBP-1 represents one member of a large, highly conserved gene family that encodes proteins demonstrating strong amino acid conservation across species. Finally, we identified a second family member that, although 77% similar to TBP-1, does not activate transcription from the promoters examined. This finding, together with the observation that TBP-1 does not activate each promoter examined, suggests that this gene family may encode promoter-specific transcriptional activators.

ATPases Associated with Diverse Cellular Activitie↗
PubMed2005

Interruption of treatment with individual therapeutic drug classes in adults with multidrug-resistant HIV-1 infection.

BACKGROUND: Many antiretroviral-treated human immunodeficiency virus (HIV)-infected patients experience sustained immunologic and virologic benefit despite the presence of multidrug-resistant HIV. We hypothesized that the use of simplified regimens could maintain treatment benefit while preventing viral evolution and reducing drug-related toxicity and costs. METHODS: We conducted a 48-week nonrandomized study of adults with multidrug-resistant HIV type 1 infection. Subjects interrupted protease inhibitor (PI) (n=18), reverse-transcriptase inhibitor (RTI) (n=6), or nonnucleoside RTI (NNRTI) (n=6) treatment. RESULTS: At study entry, subjects had a median reduction in HIV RNA levels of 1.2 log10 copies/mL relative to pretreatment levels. Interruption of PI treatment was associated with stable HIV RNA levels (mean change per week, +0.005 log10 copies/mL; P=.36). PI mutations waned and replicative capacity and HIV RNA levels increased after long-term observation. HIV RNA levels also remained stable in subjects interrupting NNRTI treatment. In contrast, all subjects who interrupted RTI treatment exhibited immediate increases in HIV RNA levels, and most exhibited a subsequent loss of the M184V mutation. CONCLUSIONS: These data indicate that nucleoside analogues often exert continued antiviral activity in the setting of drug-resistance mutations and that both nucleoside analogues and PIs can select for drug-resistance mutations that reduce viral fitness. These observations support the evaluation of treatment strategies aimed at maintaining the treatment benefit of therapy while reducing drug exposure.

Anti-Retroviral Agents↗
PubMed2025

The R203M and D377Y mutations of the nucleocapsid protein promote SARS-CoV-2 infectivity by impairing RIG-I-mediated antiviral signaling.

The viral protein mutations can modify virus-host interactions during virus evolution, and thus alter the extent of infection or pathogenicity. Studies indicate that nucleocapsid (N) protein of SARS-CoV-2 participates in viral genome assembly, intracellular signal regulation and immune interference. However, its biological function in viral evolution is not well understood. SARS-CoV-2 N protein mutations were analyzed in Delta, Omicron, and original strains. Two mutations with a methionine (M) residue at site 203 and a tyrosine (Y) residue at site 377 of the N protein were found in Delta strain but not in Omicron and original strains, and promoted SARS-CoV-2 infection therein. Those mutations, R203M and D377Y, enhanced the inhibitory impact of N protein on the impairment of RIG-I-mediated antiviral signaling, such as IRF3 phosphorylation and IFN-β activation. The viral RNA-binding activity of N protein was promoted by these mutations, effectively attenuating the recognition and interaction of RIG-I with viral RNA compared to the original or other variants. The R203M/D377Y mutations thus enhanced the suppressive activity of the N protein on RIG-I-mediated interferon induction both in vitro and in vivo, which in turn promoted viral replication. This study helps to understand the variability of SARS-CoV-2 in regulating host immunity.

SARS-CoV-2↗
PubMed2002

The origin of DNA genomes and DNA replication proteins.

In recent years, it has became clear that most proteins involved in cellular DNA precursor synthesis or DNA replication have been 'invented' more than once, indicating that the transition from RNA to DNA genomes was more complex than previously thought. Several authors have suggested that DNA viruses, which often encode their own version of these proteins, played an important role in this process. The nature of the genome of the last universal cellular ancestor (LUCA) -- that is, RNA or DNA, prokaryotic-like or eukaryotic-like -- remains in dispute. A hyperthermophilic LUCA would have suggested a circular, double-stranded DNA genome; however, recent data favor a mesophilic or moderately thermophilic LUCA.

Biological Evolution↗
PubMed2005

High doses of siRNAs induce eri-1 and adar-1 gene expression and reduce the efficiency of RNA interference in the mouse.

RNAi (RNA interference) is a gene-silencing mechanism that is conserved in evolution from worm to human and has been a powerful tool for gene functional research. It has been clear that the RNAi effect triggered by endogenous or exogenous siRNAs (small interfering RNAs) is transient and dose-dependent. However, there is little information on the regulation of RNAi. Recently, some proteins that regulate the RNA-silencing machinery have been identified. We have observed in previous work that the expression of target genes rebounds after being suppressed for a period of time by siRNAs. In the present study, we used secretory hepatitis B virus surface antigen gene as a reporter and compared its expression level in cell culture and mice challenged by different doses of siRNAs. A quicker and higher rebound of gene expression was observed in mice tail-vein-injected with higher doses of siRNA, and the rebound was associated with an increase in the mRNA level of meri-1 (mouse enhanced RNAi) and adar-1 (adenosine deaminase acting on RNA) genes encoding an exonuclease and RNA-specific adenosine deaminase respectively. Down-regulation of meri-1 by RNAi enhanced the sensitivity and efficiency of siRNA in inhibiting the expression of hepatitis B virus surface antigen. These results indicate that RNAi machinery may be under negative regulation, through the induction of a series of genes coding for destabilizing enzymes, by siRNAs introduced into the cell, and also suggest that a suitable amount of siRNA should be used for research or therapeutic applications.

Adenosine Deaminase↗
PubMed1977

Biochemical and immunological properties of gag genecoded structural proteins of endogenous tyep C RNA tumor viruses of diverse mammalian species.

The major nonglycosylated structure proteins of mammalian type C RNA tumor viruses are synthesized in the form of a high molecular weight precursor coded for by a viral gene disignated "gag". Previous genetic analysis of a prototype virus isolated of mouse origin has led to a determination of the internal arragnement of the regions within the gag gene coding for individual structural proteins. In the present study, the biochemical properties of structural proteins of type C virus isolates of additional mammalian species were analyzed. The results obtained indicate that the biochemical properties of immunologically cross-reactive proteins have been highly conserved throughout the evolution of this group of viruses. Moreover, these findings provide a means of mapping the gag genes of a broad range of mammalian type C viruses. In view of the results obtained, a new nomenclature system for type C viral gag gene-coded translational products is proposed.

Animals↗