Transcriptomics is the investigation of a set (or all) RNA molecules, including mRNA, rRNA, tRNA, and non-coding RNA produced in one or a population of cells (see Wikipedia for more informations). Metatranscriptomics is expanding this research to cells of multiple organisms, which are analysed in parallel, like for example in environmental samples.
My research interest is focused on fungal transcripts (especially mRNAs) in specific cultures or soil samples. In these samples I want to detect fungal activity, i.e. the analysis of fungal mRNAs that encode for example extracellular enzymes. Hereby we apply more “classical” procedures, like screening of transcriptomic libraries using yeast mutants, either by functional complementation or the extracellular detection of enzymes using different substrates. Using this approach we avoid cost-, time- and computer-intense high-throughput (next-generation) sequencing techniques. However, the later approach will be crucial for our understanding of environmental processes in near future. We therefore installed an Ion Torrent platform [link] in our lab.
At the moment we use several approaches: i) the analyses of fungal transcripts in cDNAs by PCR with degenerate primers, hereby comparing different soil samples, ii) the analysis of all mRNA transcripts using semiconductor sequencing (Ion Torrent) and iii) the complementation of yeast mutants using metatranscriptomic libraries. The first approach is sequence based, the second approach transcriptome focussed (RNA-seq) and the third focuses on detection and sequencing of single or few positive candidates (full length genes).
Of course all approaches have limitations and need steady improvement (discussed in the publications).
Finally we use the transcriptome information to access the proteome or more specifically the fungal secretome.
Here I want present some results of studies using transcriptomes of diverse fungi or metatranscriptomes of environmental samples.
section A: Fungal cultures
A1: (Maira study, soon)
section B: Environmental samples
B1: Detection of acid phosphatase by complemtation of a yeast pho5- mutant. [link]
i) accessing the fungal metatranscriptome using degenerate primers [link]
ii) regulation of laccase and cellobiohydrolase in forest soil under increased N deposition [link]
Bailly J, Fraissinet-Tachet L, Verner MC, Debaud JC, Lemaire M, et al. (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 1: 632–642.
Damon C, Vallon L, Zimmermann S, Haider MZ, Galeote V, Dequin S, Luis P, Fraissinet-Tachet L, Marmeisse R (2011) A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J. 5 (12):1871-80
Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L, Marmeisse R (2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS One. 7 (1):e28967
Edwards I.P., Zak D.R., Kellner H., Eisenlord S.D., Pregitzer K.S. (2011): Simulated atmospheric N deposition alters fungal community composition and suppresses ligninolytic gene expression in a northern hardwood forest. PLoS ONE 6(6): e20421.
I have to thank Micheline Vandenbol, Daniel Portetelle, Sebastian Steels, Rene Martin, Maira and the Hofrichter lab.