Methods to estimate the proportion of plant and fungal RNA in an arbuscular mycorrhiza

Arbuscular mycorrhizas are endosymbiotic associations formed between obligately biotrophic arbuscular mycorrhizal (AM) fungi and plant roots. The fungus and plant coexist in intimate contact as the fungus grows within the cortex of the root. RNA isolated from arbuscular mycorrhizas contains transcripts from both eukaryotic genomes. It is essential to be able to estimate the relative levels of fungal and plant RNA so that changes in plant and fungal gene expression can be evaluated during development of the AM symbiosis. Here we describe the design and use of specific plant and fungal internal transcribed spacer sequences and 18S rRNA probes to distinguish and quantify the relative levels of RNA of plant and fungal origin in samples from arbuscular mycorrhizas. We present two different methods. The first employs the most traditional method of transcript level analysis, namely northern blot analysis. The second one uses ribonuclease protection assays, which permit the analysis of transcript levels in a very small amount of tissue and are proving to be suitable for the analysis of gene expression in AM fungi. Analysis of tissues from a developing mycorrhiza showed that the relative levels of fungal RNA increased gradually as colonization of the root system progressed, reaching 5-12% in the most highly colonized samples.