Role of the GRAS transcription factor ATA/RAM1 in the transcriptional reprogramming of arbuscular mycorrhiza in Petunia hybrida
Melanie K. Rich, Pierre-Emmanuel Courty, Christophe Roux and Didier Reinhardt|Department of Biology, University of Fribourg, Rte Albert-Gockel 3, 1700 Fribourg, Switzerland, Laboratoire de Recherche en Sciences Vegetales, Universite de Toulouse, CNRS, UPS, 24 Chemin de Borde Rouge-Auzeville, 31326 Castanet-Tolosan, France|BMC Genomics|2017|18:589 DOI 10.1186/s12864-017-3988-8
Arbuscular mycorrhiza (AM) is a symbiosis between plants and soil borne fungi that improves water and nutrient (e.g. nitrogen, sulphur and phosphorus) supply to the host plant, whilst 20% of the plant-fixed carbon is returned to the fungus. Symbiosis occurs through structures inside plant root cells known as arbuscules, where the development of these structures occurs by an exchange of signalling molecules between the symbionts. Previous studies using several host model species have shown that a set of conserved genes is induced in mycorrhizal roots. As many genes are involved in mycorrhizal root functions, transcriptional factors, such as CYC and RAM1, are expected to play a critical role in AM-related gene induction. In this study, a transcript profiling experiment by RNA sequencing on Petunia hybrida was done to observe what level of the AM interaction RAM1 acts in. Illumina HiSeq mRNA sequencing was performed by Beckman Coulter Genomics and the reads were trimmed for quality and aligned to the reference transcripts. The unique and total mapped number of reads for each transcript was determined and then normalized to RPKM. The expression of each transcriptional factor was compared between mycorrhizal and control treatment, where genes were considered differentially expressed if the induction ratio was 2-fold different. This was backed up by performing a relative expression experiment on the Mic qPCR cycler. The REST method was used, where the GAPDH gene was used as the reference gene. The results indicated that the genes involved at early stages of AM were not affected by the RAM1 mutation but rather genes in involved at later stages, for example for nutrient exchange in cortex cells. Reduction in expression was particularly seen in genes involved in arbuscule functioning (e.g. PT4 and STR). A large number of GRAS proteins were also observed to be induced in mycorrhizal roots.