Inside Arbuscular Mycorrhizal Roots – Molecular Probes to Understand the Symbiosis

Abstract

Associations between arbuscular mycorrhizal (AM) fungi and plants are an ancient and widespread plant microbe symbioses. Most land plants can associate with this specialized group of soil fungi (in the Glomeromycota), which enhance plant nutrient uptake in return for C derived from plant photosynthesis. Elucidating the mechanisms involved in the symbiosis between obligate symbionts such as AM fungi and plant roots is challenging because AM fungal transcripts in roots are in low abundance and reference genomes for the fungi have not been available. A deep sequencing metatranscriptomics approach was applied to a wild-type tomato and a tomato mutant (Solanum lycopersicum L. cultivar RioGrande 76R) incapable of supporting a functional AM symbiosis, revealing novel AM fungal and microbial transcripts expressed in colonized roots. We confirm transcripts known to be mycorrhiza associated and report the discovery of more than 500 AM fungal and novel plant transcripts associated with mycorrhizal tomato roots including putative Zn, Fe, aquaporin, and carbohydrate transporters as well as mycorrhizal-associated alternative gene splicing. This analysis provides a fundamental step toward identifying the molecular mechanisms of mineral and carbohydrate exchange during the symbiosis. The utility of this metatranscriptomic approach to explore an obligate biotrophic interaction is illustrated, especially as it relates to agriculturally relevant biological processes.

An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts

“…All the selected proteins corresponded to Medicago truncatula proteins (Table S6); they exhibited at least one peptide with oxidized methionine residues. Putting together these results and data from the transcriptomic analysis of mycorrhizal roots, revealing that only a small number of fungal transcripts (2.5%) are detectable (Ruzicka et al ., ), we may conclude that the carbonylated proteins detected in the mycorrhizal roots are mostly of plant origin.…”

Advances in tomato research in the post-genome era

“…Moummou et al 2012, Yarmolinsky et al 2013, Kachanovsky et al 2012, Chalivendra et al 2013, Fujisawa et al 2013 RNaseq annotation Epigenetics and expression Genomic methylation Zhong et al 2013, Karlova et al 2013, Van Vu et al 2012, Ruzicka et al 2012, Gupta et al 2013, Kumar et al 2012, Tzfadia et al 2012, Quadrana et al 2013, Sablok et al 2013, Cigliano et al 2013, Osorio et al 2013, Hendelman et al 2013 miRNA and transcript identification Tissue specific expression Gene and networks prediction Protein expression Phenotype to genotype Trait-specific marker development Sharlach et al 2013, Sim et al 2012b, Kadirvel et al 2013, MacAlister et al 2012, Chibon et al 2012 Asamizu et al 2012, Di Matteo et al 2013, Andolfo et al 2013, Góngora-Castillo et al 2012, Shirasawa et al 2010, Sugita et al 2013, Wei et al 2012, Wang et al 2013, Shahin et al 2012, Goulet et al 2012, De Smet et al 2013 Candidate gene prediction Resequencing Gene and sequence conservation Comparative mapping Orthologs mapping Figure 1. Word cloud generated from titles and keywords of peer-reviewed papers citing the tomato genome.…”

“…To this end, the tomato genome has been useful in many studies. For example, reads from wild type and mutant tomatoes grown in soil where arbuscular mycorrhizal fungi were present were mapped to the genome to ensure the reads were from tomato and to identify novel transcripts (Ruzicka et al 2012). SUN, OFP, GABBY transcription factor expression was analyzed by mapping reads to the tomato genome to determine that some may exhibit tissue-specific expression and there are chromosomal locations enriched with these genes .…”

Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening

“…New platforms, including high throughput sequencing, have recently revealed the wide molecular reprogramming that occurs during mycorrhizal symbiosis and allowed the description of a set of mycorrhiza-induced root-specific genes. These genes regulate not only nutrient transport, but also carbohydrate and lipid metabolism as well as cell wall remodeling (Ruzicka et al 2013). Extending transcriptomic analysis to the whole plant, an organ-independent gene core set and a systemic defencerelated gene program have been detected in shoot and fruits, both induced by the presence of AMF (Fiorilli et al 2009;Salvioli et al 2012).…”