Identification and Genesis of a Cluster of Fungal Pathogenicity Genes

University Of Arizona, Tucson AZ

Investigators

Abstract

This research has the potential to identify a new class of pathogenicity genes in fungi and to further the understanding of the genomic organization and transmission of these genes. Whereas the horizontal transfer of groups of genes, as exemplified by bacterial pathogenicity islands, is well accepted as a phenomenon and an evolutionary driving force in bacterial pathogens of plants and animals, its role in the evolution of fungal pathogenicity is controversial. The studies on the genesis of the PEP cluster, a group of genes involved in the pathogenicity of the fungus Nectria haematococca on pea, will contribute to the understanding of the evolution of pathogenicity and help to determine whether fungi can acquire pathogenicity genes by horizontal transfer. The PEP cluster is located on a 1.6-Mb conditionally dispensable (CD) chromosome, which is dispensable for growth in culture but is required for growth in specific habitats, in this case pea tissue. The prototype PEP cluster contains six genes that are expressed during the infection of pea. A survey of 25 field isolates has revealed that all highly virulent isolates have all members of the cluster, while none of the non-virulent isolates contains the entire cluster. Recently, six additional ORFs, which are expressed during infection, have been identified in the regions flanking the prototype PEP cluster. When the codon bias of these genes and 21 genes from non-CD (N) chromosomes were compared using a cluster algorithm, two distinct groups with a high degree of correlation to the sources of the genes were identified. These differences in DNA structure between the genes in the PEP region and the genes from the other chromosomes are consistent with the hypothesis that the PEP cluster, and perhaps the entire CD chromosome, are of exogenous origin. The objectives of this project are to characterize further the contributions made to virulence by each gene in the PEP cluster, including the newly identified ORFs in the regions flanking the cluster, and to determine if these genes and the CD chromosome upon which they reside were acquired by horizontal transfer. To address the question of horizontal gene transfer, the DNA sequences of approximately one hundred additional genes from both the N and CD chromosomes will be obtained and their characteristics (e. g. G+C content, codon usage, frequency of di- and tri- nucleotides, and 3:1 dinucleotide bias) will be compared utilizing multivariate analysis. The physical locations and organization of the PEP homologues in isolates with different pathogenicity phenotypes will be determined to gain insight into events that may have lead to the formation and/or fragmentation of the cluster. Finally, the phylogenetic distribution of the PEP genes and other genes from the CD chromosome will be analyzed to extend preliminary results that showed a discontinuous distribution, a result that is consistent with horizontal gene transfer. This project addresses basic questions on the evolution of fungal genomes. In addition, the identification of pathogenicity traits and knowledge about how fungi acquire them may directly affect the current methods for the control of these agricultural pests and aid in the design of new strategies to prevent plant diseases. Undergraduates from the University of Arizona and from Luther College, one of six liberal arts colleges participating in the Department of Plant Pathology's "Winter Internship Program", will participate in this research. Funds from this grant will enable these Luther College students to carry out hands-on research utilizing contemporary technologies at their home institution.