Previously we demonstrated frequent homologous crossovers among molecules of the RNA3 segment in the tripartite brome mosaic bromovirus (BMV) RNA genome (A. Bruyere, M. Wantroba, S. Flasinski, A. Dzianott, and J. J. Bujarski, J. Virol. 74:4214-4219, 2000). To further our knowledge about mechanisms of viral RNA genome variability, in this paper we have studied homologous recombination in BMV RNA1 and RNA2 components during infection. We have found that basal RNA-RNA crossovers could occur within coding regions of both RNAs, although recombination frequencies slightly varied at different RNA sections. In all cases, the frequencies were much lower than the rate observed for the intercistronic recombination hot spot in BMV RNA3. Probability calculations accounted for at least one homologous crossover per RNA molecule per replication cycle. In addition, we have demonstrated an efficient repair of mutations within the conserved 3 and 5 noncoding regions, most likely due to error-prone BMV RNA replication. Overall, our data verify that homologous crossovers are common events a during virus life cycle, and we discuss their importance for viral RNA genetics.Enormous genetic variability is one of the unusual features of RNA viruses. Numerous experiments reveal two main sources of genetic polymorphism that contribute to the rapid evolution of RNA viruses: error-prone replication and RNA recombination (25). The former introduces into the viral RNA genome a wide spectrum of point mutations at the rate of 10 Ϫ4 to 10 Ϫ5 per nucleotide per replication cycle (33, 34). The latter is a widespread phenomenon described in many groups of RNA viruses, including picornaviruses (3,16,20), coronaviruses (5, 41), and alphaviruses (15) and in plant viruses: plum pox potyvirus (9), bromoviruses (4, 7, 8, 13), alfalfa mosaic virus (36), cucumber mosaic virus (CMV) (1, 10), tobacco mosaic virus (2), turnip crinkle virus (29, 30), and tomato bushy stunt tombusvirus (38). RNA recombination is also seen in bacteriophage Q (31), in negative RNA viruses (11), in double-stranded RNA viruses (35), and in retroviruses (17, 24) as well as during the formation of defective interfering RNAs (38).In spite of intensive studies, the mechanism of RNA recombination is not well understood. The copy choice mechanism, which is the most widely accepted (21), assumes that RNA recombinants result from template switching by viral RNA polymerase (RdRp) during RNA replication. Depending on the primary structure of the recombining molecules and on the location of junction sites, two types of recombination events have been recognized: homologous and nonhomologous (21), with the former being 10-fold higher than the latter in the case of brome mosaic bromovirus (BMV) (26).There is little information about homologous recombination in natural virus populations, because recombination products do not differ from parental RNAs. The crossovers in poliovirus RNA tended to occur within potential inter-and intramolecular heteroduplex regions (3, 20), whereas in mouse hepatitis ...
Despite extraordinary progress that has recently been made in biomedical sciences, viral infectious diseases still remain one of the most serious world health problems. Among the different types of viruses, those using RNA as their genetic material (RNA viruses and retroviruses) are especially dangerous. At present there is no medicine allowing an effective treatment of RNA-based virus infections. Many RNA viruses and retroviruses need only a few weeks to escape immune response or to produce drug-resistant mutants. This seems to be the obvious consequence of the unusual genetic variability of RNA-based viruses. An individual virus does not form a homogenous population but rather a set of similar but not identical variants. In consequence, RNA-based viruses can easily adapt to environmental changes, also those resulting from immune system response or therapy. The modifications identified within viral genes can be divided into two groups: point mutations and complex genome rearrangements. The former arises mainly during error-prone replication, whereas RNA recombination and generic reassortment are responsible for the latter. This article shortly describes major strategies used to control virus infections. Then, it presents the various mechanisms generating the genetic diversity of RNA-based viruses, which are most probably the main cause of clinical problems.
One of the most unusual features of RNA viruses is their enormous genetic variability. Among the different processes contributing to the continuous generation of new viral variants RNA recombination is of special importance. This process has been observed for human, animal, plant and bacterial viruses. The collected data reveal a great susceptibility of RNA viruses to recombination. They also indicate that genetic RNA recombination (especially the nonhomologous one) is a major factor responsible for the emergence of new viral strains or species. Although the formation and accumulation of viral recombinants was observed in numerous RNA viruses, the molecular basis of this phenomenon was studied in only a few viral species. Among them, brome mosaic virus (BMV), a model (+)RNA virus offers the best opportunities to investigate various aspects of genetic RNA recombination in vivo. Unlike any other, the BMV-based system enables homologous and nonhomologous recombination studies at both the protein and RNA levels. As a consequence, BMV is the virus for which the structural requirements for genetic RNA recombination have been most precisely established. Nevertheless, the previously proposed model of genetic recombination in BMV still had one weakness: it could not really explain the role of RNA structure in nonhomologous recombination. Recent discoveries concerning the latter problem give us a chance to fill this gap. That is why in this review we present and thoroughly discuss all results concerning nonhomologous recombination in BMV that have been obtained until now.
Accumulating evidence suggests that certain features of hepatitis C virus (HCV), especially its high genetic variability, might be responsible for the low efficiency of anti-HCV treatment. Here, we present a bioinformatic analysis of HCV-1a populations isolated from 23 children with chronic hepatitis C (CHC) subjected to interferon–ribavirin therapy. The structures of the viral quasispecies were established based on a 132-amino-acid sequence derived from E1/E2 protein, including hypervariable region 1 (HVR1). Two types of HCV populations were identified. The first type, found in non-responders, contained a small number of closely related variants. The second type, characteristic for sustained responders, was composed of a large number of distantly associated equal-rank variants. Comparison of 445 HVR1 sequences showed that a significant number of variants present in non-responding patients are closely related, suggesting that certain, still unidentified properties of the pathogen may be key factors determining the result of CHC treatment.Electronic supplementary materialThe online version of this article (doi:10.1007/s00705-010-0789-7) contains supplementary material, which is available to authorized users.
Sorghum is a crop plant that is grown for seeds, sucrose, forage and biofuel production. In all these applications, lignin is a superfluous component that decreases the efficiency of technological processes. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is an enzyme involved in monolignol synthesis that affects the efficiency of lignification and lignin composition. The sorghum genome harbors one CCoAOMT gene and six closely related CCoAOMT-like genes. The structures of four sorghum CCoAOMT-like enzymes suggest that these proteins might methylate caffeoyl coenzyme A and contribute to monolignol synthesis. In this study, two sorghum genes, CCoAOMT and one CCoAOMT-like, were found to be highly expressed in leaves, stems and immature seeds. The promoters of these genes possess clusters of transcription factor-binding sites specific for lignification, and this suggests that they are important for lignification. Phylogenetic analysis revealed that one sorghum CCoAOMT-like enzyme is closely related to ancestral cyanobacterial CCoAOMT-like proteins. The remaining CCoAOMT-like enzymes, including the one highly expressed in the leaves and stem, are closely related to CCoAOMT. Genes from these two groups possess different, evolutionarily conserved gene structures. The structure of the sorghum CCoAOMT-like protein from the ancestral clade was modeled and differences between enzymes from the two clades were analyzed. These results facilitate a better understanding of the evolution of genes involved in lignification, and provide valuable data for sorghum improvement through traditional breeding or molecular genetic techniques. The findings suggest that CCoAOMT-like genes might be recruited in lignification and raise questions of the frequency of such functional shifts.Electronic supplementary materialThe online version of this article (10.1007/s00438-018-1441-6) contains supplementary material, which is available to authorized users.
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