Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology

Abstract

SUMMARYPeer-reviewed literature is today littered with exciting new tools and techniques that are being used in all areas of biology and medicine. Transcriptomics, proteomics and, more recently, metabolomics are three of these techniques that have impacted on fungal plant pathology. Used individually, each of these techniques can generate a plethora of data that could occupy a laboratory for years. When used in combination, they have the potential to comprehensively dissect a system at the transcriptional and translational level. Transcriptomics, or quantitative gene expression profiling, is arguably the most familiar to researchers in the field of fungal plant pathology. Microarrays have been the primary technique for the last decade, but others are now emerging. Proteomics has also been exploited by the fungal phytopathogen community, but perhaps not to its potential. A lack of genome sequence information has frustrated proteomics researchers and has largely contributed to this technique not fulfilling its potential. The coming of the genome sequencing era has partially alleviated this problem. Metabolomics is the most recent of these techniques to emerge and is concerned with the non-targeted profiling of all metabolites in a given system. Metabolomics studies on fungal plant pathogens are only just beginning to appear, although its potential to dissect many facets of the pathogen and disease will see its popularity increase quickly. This review assesses the impact of transcriptomics, proteomics and metabolomics on fungal plant pathology over the last decade and discusses their futures. Each of the techniques is described briefly with further reading recommended. Key examples highlighting the application of these technologies to fungal plant pathogens are also reviewed.

Integration of Metabolic Reactions and Gene Regulation

“…Rossouw et al [115] measured the timecourse gene expression levels and volatile aroma compound concentrations during the fermentation processes of five industrial wine yeast strands. Reviews on systems biology studies of fungal phytopathology [116], Aspergilli [117], and micro-organisms in general [118] can also be found. Moreover, applications of high-throughput assays to the constitutive micro-organisms in an ecosystem (metagenomics, meta-transcriptomics, meta-metabolomics) are in the incipient yet accelerating stage [119].…”

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

“…We compared RNA-seq expression profiles of both fungi grown on artificial media enriched with host-derived carbon sources (poplar leaf extract or poplar wood chips). Inoculation of host-derived media has been widely used to efficiently mimic conditions occurring during host infection and colonization by fungal pathogens (18). Even if artificial media does not completely mimic the structure and dynamics of the nutritional environment that exists in planta (18,19), we expect that our simplified model of growth on poplar-enriched artificial media can provide a convenient way to compare factors involved in leaf and woody tissue invasion, breakdown, and assimilation.…”

Aquatic Fungi

“…However, in many cases, all we know of newly discovered species is the sequence of a small part of their genome, with no insights regarding morphology, physiology or ecology of the specimen. In the future, a combination of techniques such as transcriptomics (Bhadauria et al, 2007), proteomics (Doyle 2011), metabolomics (Tan et al, 2009) may allow us to evaluate physiological and ecological inferences based on DNA sequences. Classical culture techniques, however, will remain important for studying morphology, preserving voucher specimens, and generally expanding our knowledge of undescribed species associated with novel sequences.…”