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At least 415 records · Page 23Linked to original sources
PubMed1999

[Molecular evolution and genotype classification of TT virus].

Based on sequences data, TTV have a partial Rep protein motifs found among Circoviridae and the conserved region of parvoviral nonstructural polypeptides (NS)-1 genes, however we could not perform phylogenetic analyses among TTV and other viruses because of few similar sequences. Putative ORF2 among G2 and G4 encoded 49 aa because of in-frame stop codon, although that of G1 encoded 202 aa. Just down-stream of the stop codon, another putative new ORF(ORF3) were found around 150 aa. A phylogenetic analysis, using the ORF1 sequences of 93 TTV obtained from various geographical areas, indicated that the virus could be classified into six different genotypes. Further studies using more than 350 isolates obtained from DDBJ showed at least nine genotypes.

Amino Acid Sequence↗
PubMed1999

[Molecular evolution and structure of eukaryotic nuclear RNA polymerase subunits in light of the exon-intron organization of their genes].

Analysis of literary data (for Saccharomyces cerevisiae, Caenorhabditis elegans, Arabidopsis thaliana, Homo sapiens, and some other Eucarya) and our data (for Schizosaccharomyces pombe) on the exon-intron organization of the genes encoding subunits of nuclear RNA polymerases showed that introns in the orthologous genes from different organisms are arranged nonrandomly, namely, their positions, if projected on the map of the comparison of the amino acid sequences of the orthologous subunits, not infrequently coincide in evolutionarily distant species. As a rule, intron positions correspond to the boundaries of the structurally conserved regions (domains) or to the sites of possible turns of the polypeptide chain. For example, introns flank the secondary structure elements in the Rpb8 subunit with the known three-dimensional structure or the structure-function modules in subunits Rpb10 and Rpc10. These facts are in agreement with the idea of the ancient origin of introns, and with the notion of evolution of ancient protein sequences through the assembly of their genes from short protoexons selected by the nature as far back as the RNA world times. Comparative analysis of the primary structures of the subunits of eukaryotic RNA polymerases allowed us to reveal a nuclear localization signal in subunit Rpb10 and some hypothetical archaeal homologues of subunit Rpc10.

Amino Acid Sequence↗
PubMed2000

Molecular evolution of the chalcone synthase multigene family in the morning glory genome.

Plant genomes appear to exploit the process of gene duplication as a primary means of acquiring biochemical and developmental flexibility. Thus, for example, most of the enzymatic components of plant secondary metabolism are encoded by small families of genes that originated through duplication over evolutionary time. The dynamics of gene family evolution are well illustrated by the genes that encode chalcone synthase (CHS), the first committed step in flavonoid biosynthesis. We review pertinent facts about CHS evolution in flowering plants with special reference to the morning glory genus, Ipomoea. Our review shows that new CHS genes are recruited recurrently in flowering plant evolution. Rates of nucleotide substitution are frequently accelerated in new duplicate genes, and there is clear evidence for repeated shifts in enzymatic function among duplicate copies of CHS genes. In addition, we present new data on expression patterns of CHS genes as a function of tissue and developmental stage in the common morning glory (I. purpurea). These data show extensive differentiation in gene expression among duplicate copies of CHS genes. We also show that a single mutation which blocks anthocyanin biosynthesis in the floral limb is correlated with a loss of expression of one of the six duplicate CHS genes present in the morning glory genome. This suggests that different duplicate copies of CHS have acquired specialized functional roles over the course of evolution. We conclude that recurrent gene duplication and subsequent differentiation is a major adaptive strategy in plant genome evolution.

Acyltransferases↗
PubMed1999

Molecular evolution of coding and non-coding regions in Plasmodium.

Recurrence analysis provides a useful tool for the characterisation of oligonucleotide usage along genomic tracts. While coding regions are characterised by a low-recurrence regimen (except in the case of intragenic repeats) introns and intergenic regions exhibit a high density of recurring oligos, and appear to be correlated from the point of view of oligonucleotide preference. By comparing homologous loci in Plasmodium falciparum and P. berghei, it can be seen that introns and intergenic regions, though exhibiting very low sequence similarity, do not drift without constraints, but maintain a consistent use of the same oligos in the two species.

Animals↗
PubMed2000

Molecular evolution of oral poliovirus vaccine strains during multiplication in humans and possible implications for global eradication of poliovirus.

The oral poliovirus vaccine (OPV) has been effectively used in the control of poliomyelitis and in the eradication of wild polioviruses. Although there are many advantages in using attenuated OPV strains in the campaign to eradicate poliomyelitis, several studies have demonstrated that there are some disadvantages such as (a) excretion by vaccines of OPV-derived polioviruses with genomic modifications known to increase the neurovirulence, (b) appearance of vaccine-associated paralytic poliomyelitis (VAPP) and other adverse effects in vaccinees, (c) occurrence of persistent infections caused by OPV-derived strains in immunodeficient patients with VAPP, (d) transmission of OPV-derived polioviruses to susceptible individuals which develop VAPP, and (e) detection of OPV-derived polioviruses in the environment, which could be a source of infection for humans in the future. Different studies indicate that it is important to consider the possibility of persistent infections and excretion of OPV-derived polioviruses for long periods by humans, and also the survival in the environment of OPV-derived polioviruses excreted by humans, which could be transmitted and circulate in a non-immune population after stopping poliovirus vaccination. The findings reported here may have important implications for global poliomyelitis eradication initiative and indicate that surveillance of OPV-derived strains will also be important in the final step of eradication of poliomyelitis from the planet.

Animals↗
PubMed2000

Iridovirus homologues of cellular genes--implications for the molecular evolution of large DNA viruses.

Iridoviruses belong to the group of large cytoplasmic deoxyriboviruses and infect either insects or vertebrates. In analogy to other large DNA viruses of eucaryotes it was found that iridoviruses encode a number of cellular protein homologues. The majority of these proteins represent orthologues of cellular enzymes involved in transcription, replication, and nucleotide metabolism. Others may have the potential to interfere with cell cycle regulation or immune defence mechanisms of the host. This raises the question about the phylogenetic origin of the corresponding viral genes. During the evolution of large cytoplasmic DNA viruses such as iridoviruses, poxviruses, and African swine fever virus the acquirement of cellular genes appears to be a crucial event. Each member of this group of viruses encodes a DNA polymerase, two subunits of the DNA-dependent RNA polymerase, and two subunits of the ribonucleotide reductase. It is important to note that all of these viral proteins show a high level of multidomain structure conservation as compared to their cellular orthologues. As a consequence the large cytoplasmic DNAviruses have the ability to replicate independently of the cellular nucleus in the cytoplasm of the infected cell. Assuming a common cellular origin of viral DNA polymerase genes the corresponding amino acid sequences were chosen to construct a phylogenetic tree showing the relatedness among large DNA viruses of eucaryotes.

Animals↗
PubMed2000

Molecular evolution, distribution and genetic relationship among the dengue 2 viruses isolated from different clinical severity.

Twenty-two strains of dengue 2 virus, isolated in China, Latin America, New Guinea and Thailand were subjected to phylogenetic analysis. The UPGMA analysis was carried out on each gene region of dengue virus and demonstrated that outcome from most of the gene regions showed similar results except those from NS4B and YUTR with very short nucleotide length. Among ten regions examined, the results from E gene documented the geographical differences of the virus strains most clearly and all the American strains (Mara 4, IQT1797 and S1) were distantly related to the Asian isolates. As for the 16 Thai strains isolated in 1993, they were clustered into three groups and a strain from a DSS patient formed a distinct branch compared to the other two groups. This finding from phylogenetic analysis is consistent with earlier conclusion and support the severity related subtyping of dengue 2 virus based on amino acid changes.

3' Untranslated Regions↗
PubMed2000

Molecular evolution of lycopene cyclases involved in the formation of carotenoids with ionone end groups.

A survey is given of the lycopene cyclase genes present in bacteria, fungi and plants where two completely unrelated types exist. One is the classical monomeric bacterial beta-cyclase gene, crtY, which may be an ancestor of crtL, the gene for a beta-cyclase in cyanobacteria. From crtL a line of evolution can be drawn to plant beta- and epsilon-cyclase genes and to the gene of capsanthin/capsorubin synthase. In Gram-positive bacteria two genes crtYc and crtYd are present. They encode two proteins which have to interact as a heterodimer for lycopene beta-cyclization. From this type of lycopene cyclase gene the fungal lycopene cyclase/phytoene synthase fusion gene evolved.

Amino Acid Sequence↗
PubMed2000

[Quasispecies and molecular evolution of viruses].

Ribonucleic acid (RNA) viruses evolve as complex distributions of genetically different but closely related variants termed viral quasispecies. The precise genome of a quasispecies cannot be defined, since the consensus genome is an average of many variants. The dynamics of quasispecies has considerable implications for the understanding of the adaptability and pathogenic potential of viruses, and in addition, for the design of preventive and therapeutic measures for the diseases caused by these viruses. The authors summarise current knowledge on the structure of quasispecies, and the biological implications of this structure.

Adaptation, Biological↗
PubMedDate not supplied

Molecular evolution: first enzymes, gases as substrates and genetic templates.

A fundamental problem in biology is the self-assembly of the first cells capable of growth and division under anoxic conditions on the Earth. Evolution proceeded by self-assembling and self-replicating cells that reproduced their own genetic information and also changed their genetic code over time. Was it also possible that some of the first proteins were catalytic and used gases as substrates and also acted as genetic templates? This paper explores the possibility that primitive protein enzymes used gases as their substrates, and reverse translation may have been a feature in the self-assembly of the first cell(s).

Cells↗
PubMed2001

Inference and prediction of courses of the diseases caused by pathologic viruses by estimating molecular evolution of within-host virus.

A new approach for inferring the evolutionary process of within-host virus is presented in this study. This approach includes a sequential-linking algorithm developed by us that can deal with the sequential viral samples that are obtained at different time points from the same host, and reconstruct a longitudinal phylogenetic tree in which the evolutionary relations between viral variants can be shown. A codon-based model, which uses a Markov process to describe substitutions between codons, is also employed in this approach to calculate synonymous and non-synonymous substitution rates and to distinguish positive selection and neutral evolution. The approach is applied to a data set of the V3 region of the HIV-1 envelope genes sequenced in different years after infection of a single patient. The results suggest that this approach may provide a more realistic description of viral evolution than the traditional evolution models because it accounts for both neutral and adaptive evolution. Most important of all, since this approach make it possible to follow up the evolutionary process of within-host virus by analyzing the sequential viral samples, it could be used in inference and prediction of the course of the diseases caused by pathologic viruses and evaluation of the treatment.

Algorithms↗