Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction

Abstract

In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root—mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with 15 transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.

The Influence of Contrasting Microbial Lifestyles on the Pre-symbiotic Metabolite Responses of Eucalyptus grandis Roots

“…In terms of tree-ECM fungal interaction models, a study by Zmasek et al (2016) has predicted the metabolic reprogramming in Populus-Laccaria interaction at early pre-symbiotic phase through in silico modeling based on transcriptomic datasets. Yet, as far as we know, our present study is one of the few assessing the global metabolite responses in tree roots during pre-symbiotic interaction with ECM fungi.…”

Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

“…Strain P. protegens Pf-5 was obtained from ATCC (American Type Cell Culture) Catalog# BAA-477], and P. fluorescens strains Pf0-1(Garbeva et al, 2011 ), SBW25 (Preston et al, 2001 ), and WH6 (Banowetz et al, 2008 ) were provided by the cited laboratories (Supplementary Table S1 ). Laccaria bicolor (strain S238N, obtained from ATCC) was cultured and maintained on Modified Melin Norkan's (MMN) media at 20°C, as described in Larsen et al ( 2016 ).…”

Agricultural practices to improve nitrogen use efficiency through the use of arbuscular mycorrhizae: Basic and agronomic aspects

“…Establishing whether there is competition for N between the plant and the AMF and identifying the underlying regulatory control mechanisms seems to be a key issue for optimizing the efficiency of the symbiotic association, notably when there is low N availability in the soil [31]. Individual or combined "omics"-based techniques [32] will provide means to decipher some of the regulatory control mechanisms. However, the interpretation and integration of the generated transcriptomic, proteomic and metabolomic data under agronomic conditions will be difficult, due to the occurrence of complex mycelial networks in a single species, that are even more complex in mixtures of several species.…”