Agricultural phytopathology

MOLECULAR EVOLUTION AND RELACIOES TAXONOMIC FAMILY BROMOVIRIDAE VIRUS PLANTS

Author: CODOÑER CORTÉS FRANCISCO MANUEL.
Year: 2005.
University: VALENCIA.
Place of defense: FACULTAD DE ECONOMIA - UNIVERSITAT DE VALÈNCIA.
Place of preparation: INSTITUTO CAVANILLES DE BIODIVERSIDAD Y BIOLOGÍA EVOLUTIVA.

Summary: The Computer has become an important tool in evolutionary studies over the past 25 aios. The increase in the use of programming and the development of new algorithms in this and other areas of biology has lIevado to generate a new scientific discipline lIamada Bioinformatics. Despite its short life as a science, millions and millions of programs have been developed and are available to researchers, focusing not only for the development of studies in the field of Molecular Evolution, but also have developed programs troubleshoot time consumed in the classification and management agencies, secuancias and structures; in predicting structures in modeling in the simulations, etc. This thesis has been snowed out a study of the Molecular Evolution of the family of viruses plants Bromoviridae. The family Bromoviridae is one of the most important families of plant viruses because their members affect a wide range of hosts and cause serious damage in the aglicultura, affecting not only fruit trees, but also many kinds of crops as in the case of cucumbers, alfalfa, Jewish, and so on. The genome of Ios family members Bromoviridae is approximately 8 Kb long, divided into three RNA's single chain of positive polarity. The RNA-1 and RNA-2 encode a single ORF (proteins P1 and P2), which are involved in the replication of the virus. In genres Ilarvirus and Cucumovirus the RNA2 encodes a second ORF, the protein P2b, which is apparently translated by an RNA subgenómico (sgRNA), and that this involved in the suppression of gene silencing, in the virulence of the virus and the systemic movement of the same through the plant. The RNA-3 is bicistrónico and owns two ORF's encoding proteins movement (MP) and the deck protein (CP), CP is being translated by a sgRNA (RNA-4). A special feature of lIarvirus and A / famovirus is lIamado phenomenon of gene activation, which is no more than the binding of protein to one end of the COP to initiate RNA virus (801 et. Al., 1971). Recent studies have questioned the current classification of this family of viruses of plants, especially the virus spotting of the zonal geraniums (PZSV), and the division of the family in three genres instead of the classic classification in four genres. These studies and uncertainties among the new findings that are getting us motivated lIevar out a study of the evolutionary family members Bromoviridae. First is lIevó out an evolutionary study of the two proteins encoded by the RNA-3. By using maximum likelihood methods were inferred amino acid substitution patterns that best explained the diversification of this family of viruses. The results indicate that the molecular evolution of the components of this family is quite complex, with each protein evolve at different rates and under different patterns of amino acid substitution. Among the differences are also included different frequencies aminoacídicas in equilibiro, heterogeneity in replacement ratios between sites and covaliación between sites. Despite these differences, the pattern of protein evolution that best fits both proteins is proposed specifically Whelan and Goldman (2001) to explain the evolution of globular proteins, including the variation in amino acid composition, frequency of invariable sites, so the heterogeneity in replacement ratios through the positions. There is also evidence of the existence of coevolucion between domains of these two proteins: the region C-term 8 inal of 1c21 protein MP has a replacement rate as that of the PA protein, 10 which may indicate that are under the same evolutionary pressure . The analysis also suggests that we have done that we can not support the hypothesis of the existence of the molecular clock in the evoluci6n of Ios components of this family, since different linages are evolving at different rates, this heterogeneity is strongest among linages within the gender of lIarvirus more than in the rest of the sexes. Another relevant results to be drawn from the results of the analysis of RNA-3, is the classification of the alfalfa mosaic virus (AMV) within the genus lIarvirus, finding 5 subgroups statistically significant within this genre. Finally, PZSV can be classified as a real component of the family Bromoviridae rather than as an ad incerta sedi. The taxonomy of Bromoviridae has also been scanned using techniques that incorporate recent information from the complete proteome. The approach chosen is based on the analysis of latent semantic, and the decomposition of eigenvalues of arrays containing peptides shared between different proteins. A clear advantage of this type of approach rests with the independence of the prior sequence alignment, because the sequences are taken as a text written in a particular language where words are small peptides and amino acids are the lyrics. Prior to the completion of the audit was to fix the problem of the dimensionality of space vector where they have to make the calculations. The results of the analysis, once fixed the problem of dimensionality, largely consistent with those obtained in the analysis of RNA-3, and suggests that the current classification of this family should be modified in several respects: (i) AMV is a real component of gender lIarvirus, and should not be considered as a separate and independent genre, (ii) PZSV must be considered as a member of the famiia Bromoviridae, (iii) lIarvirus should be divided into at least seven subgroups that includes the current calsificación which is made of antigenic differences. The taxonomic exact location of certain viruses in the family depends on protein is implying that the phylogenetic tree. In order to provide an explanation for the discrepancies found between the four genealogies, we performed an analysis to test possible events segregation is not independent of the RNA's events coinfección viral, as well as possible recombination events. To test the role of the recombination in the evolution of the family used two approaches based on probabilities maximo-verosimiles. The first, a Bayesian approach which identifies cut points in a set sequence alignment, and a second approach that identifies these points cut in triplets sequence alignment. The analysis we conducted showed some evidence of recombination in some family members. Especially interesting is the case of AMV, that Ios results suggest that this virus may have suffered a recombination event at the CP protein within the RNA-3 between lIarvirus and Cucumovirus. This result is also supported by certain aspects and biological characteristics that make this virus from the rest of Ios Jarvirus. Other events of recombination found in the analysis are: (i) in the protein MP PZSV between a lIarvirus and Bromovirus, (ii) in the bromine mosaic virus (BMV) is detected at the level of protein P2 possibly between Bromovirus and Cucumovirus, and (iii) in the C-terminal region of the protein P2 virus dwarfism of 10S peanuts (pSV). The results of segregation were inconclusive and therefore support the idea that RNA's segregaban independently events coinfection. Little is known about the movement of the virus ringing necrotic of prunus (PRNSV), but there is indirect evidence suggesting the involvement of the proteins encoded by the RNA-3 in this function. One aim of the thesis has been to develop a study to highlight 10 amino acids of the protein MP and CP that are involved in this important role. The importance structural and / or functional relative Ias different positions aminoacídicas in a protein can be determined by assessing the level of selective restrictions to which these amino acids are subject during the course of evolution. In one part of the thesis explores such restrictions at linear and three-dimensional proteins in MP and CP. It ámpliamente accepted that these proteins must interact to facilitate the movement viral cell to cell, but have not yet offered direct evidence. Using an approximation máximo-parsímnica were analyzed nucleotide sequences of 46 isolates PNRSV, Ios which differ in symptomatology, host and geographical origin. With the analysis have been detected in several sites both proteins that are under different pressure screening. Once detected these sites, developed an analysis of covariance to explore whether changes in certain positions of the protein variation conditioned elsewhere either the same or other protein. These analysis of covariance spread the light to see which particular amino acid position should be involved in the physical and functional interaction between proteins MP and CP. The positions are found for the C-terminal region of the protein MP and two regions of the COP, an N-terminal region and one that belongs to the amino acids ranging from position 140 to 145. Since nothing is known about the three-dimensional structure of both proteins, a method based on "thereading" was used to obtain a structure in which they can identify those amino acids have been detected in the selection and analysis of covariance, predicted These structures are in agreement certain structural characteristics described by others, finally these discoveries were contrasted with what is known about the involvement of certain sites and domains in the structure, interactions proteícas and interactions proteína-RNA.

AGRICULTURAL PHYTOPATHOLOGY