Title: Chorismate mutase: an alternatively spliced parasitism gene and a diagnostic marker for three important Globodera nematode species Authors
Submitted to: European Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 27, 2010
Publication Date: January 1, 2011
Citation: Yu, H., Chronis, D.N., Lu, S., Wang, X. 2011. Chorismate mutase: an alternatively spliced parasitism gene and a diagnostic marker for three important Globodera nematode species. European Journal of Plant Pathology. 129:89-102. Interpretive Summary: The two species of potato cyst nematode (PCN, Globodera rostochiensis and G. pallida) are significant quarantine pests causing serious problems in potato production and trade worldwide. In recent years new detections of PCN have been reported in both the U.S. and Canada, revealing an increasing threat of these pests to the potato industry in North America. The tobacco cyst nematode (TCN, G. tabacum), a closely related species of PCN, is also an important nematode pest which has been found in tobacco production areas of the U.S., Canada, Mexico, and many European countries. In order to establish a successful parasitic association with host plants, these nematodes secret proteins encoded by parasitism genes to manipulate host plant cells into a specialized site for the nematode to feed. The chorismate mutase (CM) gene is an important nematode parasitism gene that has been cloned from the two PCN species. This work reported the isolation of a new CM gene from TCN. We further analyzed the genomic structure of the CM genes from these three Globodera nematode species. Based on sequence variations observed, we developed highly specific and sensitive TaqMan qPCR assays for the identification of each Globodera species, providing an exciting example of using nematode parasitism genes as a valuable diagnostic marker for plant-parasitic nematodes. The high degree of specificity and sensitivity of these assays may permit nematode detection in soil extracts that contain extremely low amounts of nematode DNA. The application of these methods for routine detection in field samples will be valuable for nematode regulatory and quarantine programs.
Technical Abstract: The chorismate mutase gene is widely distributed in both cyst and root-knot nematode species and believed to play a critical role in nematode parasitism. In this study, we cloned a new chorismate mutase gene (Gt-cm-1) from Globodera tabacum and further characterized the gene structure in both G. tabacum and G. pallida, a closely related species of G. rostochiensis. The genomic clones of chorismate mutase genes from these two species were found to contain three introns with the second intron having unusual 5’ and 3’ splice sites. A previous study revealed that the chorismate mutase gene from G. rostochiensis is subject to alternative splicing through retention of intron 2, a process that allows for the generation of multiple mRNA transcripts from a single gene. As expected, we discovered that alternative splicing of the chorismate mutase gene is a conserved event in three Globodera species, supporting an important role of alternative splicing in regulating chorismate mutase gene function in plant parasitism by these nematodes. In addition to the potential suboptimal 5’ and 3’ splice sites and the small size of intron 2, detailed sequence analysis also identified candidate cis-acting elements that might be responsible for regulating intron retention of Globodera chorismate mutase genes. Based on genomic sequence variations observed, we developed TaqMan qPCR assays that provided a highly specific and sensitive identification of each Globodera species, revealing a new application of using the chorismate mutase gene as a valuable diagnostic marker for plant-parasitic nematodes.