Identification and Genesis of a Cluster of Fungal Pathogenicity Genes

真菌致病基因簇的鉴定和起源

• 批准号: 0239282
• 负责人: Hans. VanEtten
• 金额: $ 39.7万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-07-01 至 2007-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0239282&HistoricalAwards=false
• 关键词: Identification; Genesis; Cluster; Fungal; Pathogenicity

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.

这项研究有可能确定一类新的真菌致病基因，并进一步了解这些基因的基因组组织和传播。虽然基因组的水平转移，例如细菌致病岛，被公认为是植物和动物细菌病原体中的一种现象和进化驱动力，但其在真菌致病性进化中的作用是有争议的。PEP基因簇是一组与赤壳菌（Nectria haematococca）对豌豆的致病性有关的基因，对PEP基因簇的起源进行研究，将有助于理解病原菌致病性的进化过程，并有助于确定真菌能否通过水平转移获得致病性基因。PEP簇位于1.6-Mb条件性染色体（CD）上，其在培养物中生长是必需的，但在特定生境（在这种情况下为豌豆组织）中生长是必需的。原型PEP簇包含在豌豆感染期间表达的六个基因。对25个田间分离株的调查显示，所有高毒力分离株都具有该簇的所有成员，而无毒力分离株都不包含整个簇。最近，在PEP原型簇的侧翼区域中已经鉴定了在感染期间表达的六个额外的ORF。当使用聚类算法比较这些基因和来自非CD（N）染色体的21个基因的密码子偏好性时，鉴定出与基因来源具有高度相关性的两个不同的组。PEP区基因和其他染色体基因之间的DNA结构差异与PEP簇，也许是整个CD染色体，是外源性起源的假设一致。该项目的目标是进一步表征PEP簇中每个基因对毒力的贡献，包括簇侧翼区域中新鉴定的ORF，并确定这些基因及其所在的CD染色体是否通过水平转移获得。为了解决水平基因转移的问题，将获得来自N和CD染色体的大约100个额外基因的DNA序列，并将它们的特征（例如：G. G+C含量、密码子使用、二核苷酸和三核苷酸的频率以及3：1二核苷酸偏倚）将利用多变量分析进行比较。将确定具有不同致病性表型的分离株中PEP同源物的物理位置和组织，以深入了解可能导致簇形成和/或片段化的事件。最后，PEP基因和其他基因从CD染色体的系统发育分布将进行分析，以扩展初步结果，显示不连续的分布，结果是一致的水平基因转移。该项目解决了真菌基因组进化的基本问题。此外，致病性性状的鉴定和真菌如何获得它们的知识可能直接影响目前控制这些农业害虫的方法，并有助于设计预防植物病害的新策略。 来自亚利桑那大学和路德学院的本科生将参加这项研究，路德学院是参加植物病理学系“冬季实习计划”的六所文科院校之一。这笔赠款的资金将使这些路德学院的学生能够在他们的家乡机构利用当代技术进行实践研究。