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PubMed1995

Evolution of T4-related phages.

Much progress has been made in understanding T-even phage biology in the last 50 years. We now know the entire sequence of T4, encoding nearly 300 genes, only 69 of which have been shown to be essential under standard laboratory conditions; no specific function is yet known for about 140 of them. The origin of most phage genes is unclear, and only 42 genes in T4 have significant similarity to anything currently included in GenBank. Comparative analysis of related phages is now being used to gain insight into both the evolutionary origins and interrelationships of these phage genes, and the functions of their protein products. The genomes of phages isolated from Tbilisi hospitals, Long Island sewage plants, the Denver zoo, and Khabarovsk show basic similarity. However, these phages show substantial insertions and deletions in a number of regions relative to each other, and closer investigation of specific sequences often reveals much more complex relationships. There are only a few cases in T4-related phages in which there is evidence for evolution through DNA duplication. These include the fibrous products of genes 12, 34, and 37; head proteins gp23 and gp24; and the Alt enzyme and its downstream neighbors. T4 also contains 13 apparent relatives of group I and group II intron homing endonucleases. Distal portions of the tail fibers of various T-even phages contain segments closely related to tail-fiber regions of other DNA coliphages, such as Mu, P1, P2, and lambda. Horizontal gene transfer clearly emerges as a major factor in the evolution of at least the tail-fiber regions, where site-specific recombination probably is involved in the exchange of host-range determinants.

Amino Acid Sequence↗
PubMed1981

Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code.

Strong rhythms with a period of three bases have been seen while correlating the relative positions of purines and pyrimidines and of the four individual bases in the complete DNA sequence of the viruses phi X174, G4 and fd. Generally weaker variations of the same type have been found in the DNA virus SV40, the plasmid pBR322, the RNA virus MS2, and elsewhere in procaryotes and eucaryotes (e.g. in a ribosomal protein gene cluster of E. coli and the sea urchin histone genes). From the interrelation of four-base with purine-pyrimidine rhythms it seems that the purine-pyrimidine relationships have a basic significance. An explanation is proposed in terms of the former use of a comma-less genetic code (i.e. readable only in one frame) of the general form RNY (R = purine, Y = pyrimidine and N = purine or pyrimidine). In spite of subsequent mutation, there appears to be still enough of the primitive messages remaining to produce these periodic variations with their characteristic properties in phase and amplitude. Particularly good evidence for this hypothesis is provided by the fact that the phases for the stronger rhythms are the same in all the genomes tested and can be successfully predicted by a simple consideration of the original RNY pattern. With regard to amplitude it can be similarly foreseen which variations will be more clearly marked than others. The observed behaviour of the amplitude as the separation between correlated bases increases is also explained by the insertions, deletions and point mutations which have occurred. Additionally it is possible to account for some notable features of the non-random use of codons for the same amino acid by this theory.

Base Sequence↗
PubMed1982

Evolutionary changes of nucleotide sequences of papova viruses BKV and SV40: they are possibly hybrids.

Complete nucleotide sequences were compared between papova viruses BKV and SV40 and the degrees of sequence divergences were compared between structurally and/or functionally different segments or genes in details. It was shown that the rate of synonymous substitution is not only very high but also approximately uniform among different genes in these viruses as in eukaryotic genes examined to date. While all the non-coding regions including the intron showed marked sequence preservation which is in sharp contrasted with the case of eukaryotic genes where the large bulk of non-coding regions evolve at a rate as rapidly as that of synonymous substitution. It is remarkable that a long continuous stretch of sequence including the putative VPX gene and a 5' half of VP2 gene showed strong homology between BKV and SV40. A close examination of the pattern of base substitutions revealed that this unusual homology was derived by recombination between the two viruses during their evolution. On the basis of the pattern of base substitutions and the bias in code word utilization, we also showed that the putative VPX gene actually could code for a functional polypeptide. In papova viruses, the 3' terminal sequence of VP2/3 gene overlaps with the 5' terminal sequence of VPI gene. The pattern of base substitutions in the overlapping segment was examined in detail in comparison with those in the non-overlapping portions of VP2/3 and VP1 genes. It was shown that the evolutionary mode of the overlapping genes is in good agreement with our previous prediction.

BK Virus↗
PubMedDate not supplied

Pattern of nucleotide substitution and the extent of purifying selection in retroviruses.

The patterns of point mutation and nucleotide substitution are inferred from nucleotide differences in three coding and two noncoding regions of retroviral genomes. Evidence is presented in favor of the view that the majority of mutations accumulate at the reverse transcription stage. Purifying selection is apparently very weak at the amino acid level, and almost nonexistent between synonymous codons. The pattern of purifying selection obeys the rules previously established in vertebrates [Gojobori T, Li W-H, Graur D (1982) J Mol Evol 18:360-369]; i.e., the magnitude of purifying selection at the amino acid level is negatively correlated with Grantham's [Grantham R (1974) Science 185: 862-864] chemical distances between the amino acids interchanged. We refute Modiano et al.'s [Modiano G, Battistuzzi G, Motulsky AG (1981) Proc Natl Acad Sci USA 78:1110-1114] hypothesis, according to which the pattern of mutation is preadapted to buffer against deleterious mutations. On the contrary, the pattern of mutation reduces the level of conservativeness from that imposed on the amino acid substitution pattern by the structure of the genetic code. The extraordinarily high rate of nucleotide substitution in retroviruses in comparison with that in other organisms is apparently caused by an extremely high rate of mutation coupled with a lack of stringent purifying selection at both the codon and the amino acid levels.

Animals↗
PubMed2000

Comparison of the genome sequences and the phylogenetic analyses of the GP78 and the Vellore P20778 isolates of Japanese encephalitis virus from India.

The nucleotide sequence of the complete genomes of two Indian isolates of Japanese encephalitis virus were compared. One of these isolates, GP78 was obtained from northern India in 1978. The other, the Vellore P20778 isolate, was obtained from southern India in 1958. There was 4.40% nucleotide sequence divergence between the two Indian isolates that resulted in a 1.86% amino acid sequence divergence. Phylogenetic analyses showed that in evolutionary terms the north Indian GP78 isolate was close to the SA14 isolate from China whereas the south Indian Vellore P20778 isolate was close to the Beijing-1 isolate, also from China. The two Indian isolates, however, appear to have evolved independently.

Brain↗
PubMed1999

Little evidence for synergism among deleterious mutations in a nonsegmented RNA virus.

Several models have been proposed to account for the segmentation of RNA viruses. One of the best known models suggests that segmentation, and mixing of segments during coinfections, is a way to eliminate deleterious mutations from the genome. However, for validity, this model requires that deleterious mutations interact in a synergistic way. That is, two mutations together should have a more deleterious effect than the result of adding their individual effects. Here I present evidence that deleterious mutations in foot-and-mouth disease virus produce a decline in fitness but that the relationship between the number of mutations fixed and the magnitude of fitness decline is compatible mainly with a nonsynergistic model. However, the statistical uncertainties associated with the data still give some room for the existence of very weak synergistic epistasis.

Aphthovirus↗
PubMed1997

On the informational content of overlapping genes in prokaryotic and eukaryotic viruses.

In genetic language a peculiar arrangement of biological information is provided by overlapping genes in which the same region of DNA can code for functionally unrelated messages. In this work, the informational content of overlapping genes belonging to prokaryotic and eukaryotic viruses was analyzed. Using information theory indices, we identified in the regions of overlap a first pattern, exhibiting a more uniform base composition and more severe constraints in base ordering with respect to the nonoverlapping regions. This pattern was found to be peculiar to coliphage, avian hepatitis B virus, human lentivirus, and plant luteovirus families. A second pattern, characterized by the occurrence of similar compositional constraints in both types of coding regions, was found to be limited to plant tymoviruses. At the level of codon usage, a low degree of correlation between overlapping and nonoverlapping coding regions characterized the first pattern, whereas a close link was found in tymoviruses, indicating a fine adaptation of the overlapping frame to the original codon choice of the virus. As a result of codon usage correlation analysis, deductions concerning the origin and evolution of several overlapping frames were also proposed. Comparison of amino acid composition revealed an increased frequency of amino acid residues with a high level of degeneracy (arginine, leucine, and serine) in the proteins encoded by overlapping genes; this peculiar feature of overlapping genes can be viewed as a way with which they may expand their coding ability and gain new, specialized functions.

Amino Acid Sequence↗
PubMed2003

Adaptation of Cucumber mosaic virus soybean strains (SSVs) to cultivated and wild soybeans.

Cucumber mosaic virus soybean strains formerly called soybean stunt virus (SSV) were inoculated onto 23 wild soybeans collected from four Asian countries to investigate their infectivity in order to improve understanding of the co-evolution of SSVs and soybean. SSV inoculation resulted in systemic infection in most of the wild soybeans used. However, an SSV strain (SSV-In), which was isolated in Indonesia, did not result in systemic infection of many of the wild soybeans distributed in southern Japan. This exceptional infectivity of SSV-In may be due to its specific adaptation to the local soybean population(s) of Indonesia, which has rarely been affected by gene flows from wild soybean. In the present study, the nucleotide sequences of the 3a and CP genes of SSV were determined, and the data were used to classify seven SSV isolates among known Cucumber mosaic virus (CMV) strains. The phylogenetic analysis showed that the seven SSVs formed a distinct cluster separated from the other CMV strains despite their different geographical origins; SSV-In was the most divergent of the seven isolates. Comparison of the rates of synonymous and nonsynonymous substitutions revealed that the SSV group had evolved faster than subgroup IA. The implications of the findings are discussed in relation to the so-called Red Queen hypothesis.

Adaptation, Physiological↗
PubMed2002

Hepatitis C virus evolutionary patterns studied through analysis of full-genome sequences.

The evolutionary patterns of hepatitis C virus (HCV), including the best-fitting nucleotide substitution model and the molecular clock hypothesis, were investigated by analyzing full-genome sequences available in the HCV database. The likelihood ratio test allowed us to discriminate among different evolutionary hypotheses. The phylogeny of the six major HCV types was accurately inferred, and the final tree was rooted by reconstructing the hypothetical HCV common ancestor with the maximum likelihood method. The presence of phylogenetic noise and the relative nucleotide substitution rates in the different HCV genes were also examined. These results offer a general guideline for the future of HCV phylogenetic analysis and also provide important insights on HCV origin and evolution.

Biological Evolution↗
PubMed2002

Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis.

The study of rates of nucleotide substitution in RNA viruses is central to our understanding of their evolution. Herein we report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method. This analysis revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Despite the lack of a molecular clock, the range of statistically significant variation in overall substitution rates was surprisingly narrow for those viruses where a significant relationship between genetic divergence and time was found, as was the case when synonymous sites were considered alone, where the molecular clock was rejected less frequently. An analysis of the ecological and genetic factors that might explain this rate variation revealed some evidence of significantly lower substitution rates in vector-borne viruses, as well as a weak correlation between rate and genome length. Finally, a simulation study revealed that our maximum likelihood estimates of substitution rates are valid, even if the molecular clock is rejected, provided that sufficiently large data sets are analyzed.

Amino Acid Substitution↗
PubMed2003

Widespread adaptive evolution in the human immunodeficiency virus type 1 genome.

We investigated variable selective pressures among amino acid sites in HIV-1 genes. Selective pressure at the amino acid level was measured by using the nonsynonymous/synonymous substitution rate ratio (omega = dN/dS). To identify amino acid sites under positive selection with omega > 1, we applied maximum likelihood models that allow variable omega ratios among sites to analyze genomic sequences of 26 HIV-1 lineages including subtypes A, B, and C. Likelihood ratio tests detected sites under positive selection in each of the major genes in the genome: env, gag, pol, vif, and vpr. Positive selection was also detected in nef, tat, and vpu, although those genes are very small. The majority of positive selection sites is located in gp160. Positive selection was not detected if omega was estimated as an average across all sites, indicating the lack of power of the averaging approach. Candidate positive selection sites were mapped onto the available protein tertiary structures and immunogenic epitopes. We measured the physiochemical properties of amino acids and found that those at positive selection sites were more diverse than those at variable sites. Furthermore, amino acid residues at exposed positive selection sites were more physiochemically diverse than at buried positive selection sites. Our results demonstrate genomewide diversifying selection acting on the HIV-1.

Amino Acid Sequence↗
PubMed2001

Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae).

Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species, such as Q beta and MS2, have been studied as model systems for replication, translation, and the role of secondary structure in gene regulation. Using nucleotide sequences from the coat and replicase genes we present the first statistical estimate of phylogeny for the family Leviviridae using maximum-likelihood and Bayesian estimation. Our analyses reveal that the coliphage species are a monophyletic group consisting of two clades representing the genera Levivirus and Allolevivirus. The Pseudomonas species PP7 diverged from its common ancestor with the coliphage prior to the ancient split between these genera and their subsequent diversification. Differences in genome size, gene composition, and gene expression are shown with a high probability to have changed along the lineage leading to the Allolevivirus through gene expansion. The change in genome size of the Allolevivirus ancestor may have catalyzed subsequent changes that led to their current genome organization and gene expression.

Allolevivirus↗
PubMed2001

Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region.

Phylogenetic analyses frequently rely on models of sequence evolution that detail nucleotide substitution rates, nucleotide frequencies, and site-to-site rate heterogeneity. These models can influence hypothesis testing and can affect the accuracy of phylogenetic inferences. Maximum likelihood methods of simultaneously constructing phylogenetic tree topologies and estimating model parameters are computationally intensive, and are not feasible for sample sizes of 25 or greater using personal computers. Techniques that initially construct a tree topology and then use this non-maximized topology to estimate ML substitution rates, however, can quickly arrive at a model of sequence evolution. The accuracy of this two-step estimation technique was tested using simulated data sets with known model parameters. The results showed that for a star-like topology, as is often seen in human immunodeficiency virus type 1 (HIV-1) subtype B sequences, a random starting topology could produce nucleotide substitution rates that were not statistically different than the true rates. Samples were isolated from 100 HIV-1 subtype B infected individuals from the United States and a 620 nt region of the env gene was sequenced for each sample. The sequence data were used to obtain a substitution model of sequence evolution specific for HIV-1 subtype B env by estimating nucleotide substitution rates and the site-to-site heterogeneity in 100 individuals from the United States. The method of estimating the model should provide users of large data sets with a way to quickly compute a model of sequence evolution, while the nucleotide substitution model we identified should prove useful in the phylogenetic analysis of HIV-1 subtype B env sequences.

Evolution, Molecular↗
PubMed2005

Molecular characterization of a virus from the family Luteoviridae associated with cotton blue disease.

Cotton blue disease is an aphid-transmitted cotton disease described in Brazil in 1962 as Vein Mosaic "var. Ribeirão Bonito". At present it causes economically important losses in cotton crops if control measures are not implemented. The observed symptoms and mode of transmission have prompted researchers to speculate that cotton blue disease could be attributed to a member of the family Luteoviridae, but there was no molecular evidence supporting this hypothesis. We have amplified part of the genome of a virus associated with this disease using degenerate primers for members of the family Luteoviridae. Sequence analysis of the entire capsid and a partial RdRp revealed a virus probably belonging to the genus Polerovirus. Based on our results we propose that cotton blue disease is associated with a virus with the putative name Cotton leafroll dwarf virus (CLRDV).

Amino Acid Sequence↗
PubMed2006

Exploration of the emergence of the Victoria lineage of influenza B virus.

The Victoria lineage represented by B/Victoria/2/87 is one of the two major distinctive haemagglutinin (HA) lineages of influenza B virus, and its recent re-emergence has aroused great concerns. However, it remains unknown when, where, and how this HA lineage emerged in the world. In this study, the HA1 domain of the HA gene of fourteen influenza B viruses isolated in China in 1972-1984 was sequenced. The sequences were phylogenetically analyzed with the HA1 sequences of 41 other important influenza B isolates. The results unveiled some earlier footprints of the Victoria lineage in China, and the epidemic history of the Victoria lineage could be traced back from the year 1985 to 1975. Moreover, phylogenetic analysis, the history of China, and the epidemiology of influenza B virus indicated that the Victoria lineage possibly emerged in China in the 1970s through gradual evolution from a minor lineage.

Amino Acid Sequence↗
PubMed1998

Analysis of genetic information of an insect picorna-like virus, infectious flacherie virus of silkworm: evidence for evolutionary relationships among insect, mammalian and plant picorna(-like) viruses.

We synthesized the cDNAs of an insect picornavirus, infectious flacherie virus of silkworm (IFV), genomic RNA and inserted it into a bacterial plasmid (pUC119). The 9,650 nucleotides (nts) sequence except for the poly(A) tail was obtained from the cloned cDNAs, and the sequence integrity was confirmed by primer extension and direct RNA sequencing. The sequence has a large open reading frame (ORF) of 9,255 nts (3,085 codons) flanked by the short 5' non-coding region (156 nts) and by the rather long 3' non-coding (239 nts). The structural proteins VP3, 4, 1 and 2 were located at the N-terminus of the polyprotein in this order and were preceded by a tentative small peptide. Computer analysis identified the sequences similar to the consensus sequences of 2C (helicase?), 3C (protease), and 3D (RNA polymerase) conserved among mammalian and plant picorna(-like) viruses. In addition, the predicted genome organization of IFV was quite similar to those of picornaviruses. Further analyses of the characteristics of the genome structure and a tentative phylogenetic tree constructed on the basis of the amino acid sequence similarity emphasized the evolutionary relationships among the insect and plant viruses.

Adenoviridae↗