Genome wide analysis of protein production load in Trichoderma reesei

Tiina M. Pakula, Heli Nygren, Dorothee Barth, Markus Heinonen, Sandra Castillo, Merja Penttilä, Mikko Arvas*

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

21 Citations (Scopus)
255 Downloads (Pure)


Background: The filamentous fungus Trichoderma reesei (teleomorph Hypocrea jecorina) is a widely used industrial host organism for protein production. In industrial cultivations, it can produce over 100 g/l of extracellular protein, mostly constituting of cellulases and hemicellulases. In order to improve protein production of T. reesei the transcriptional regulation of cellulases and secretory pathway factors have been extensively studied. However, the metabolism of T. reesei under protein production conditions has not received much attention. Results: To understand the physiology and metabolism of T. reesei under protein production conditions we carried out a well-controlled bioreactor experiment with extensive analysis. We used minimal media to make the data amenable for modelling and three strain pairs to cover different protein production levels. With RNA-sequencing transcriptomics we detected the concentration of the carbon source as the most important determinant of the transcriptome. As the major transcriptional response concomitant to protein production we detected the induction of selected genes that were putatively regulated by xyr1 and were related to protein transport, amino acid metabolism and transcriptional regulation. We found novel metabolic responses such as production of glycerol and a cellotriose-like compound. We then used this cultivation data for flux balance analysis of T. reesei metabolism and demonstrate for the first time the use of genome wide stoichiometric metabolic modelling for T. reesei. We show that our model can predict protein production rate and provides novel insight into the metabolism of protein production. We also provide this unprecedented cultivation and transcriptomics data set for future modelling efforts. Conclusions: The use of stoichiometric modelling can open a novel path for the improvement of protein production in T. reesei. Based on this we propose sulphur assimilation as a major limiting factor of protein production. As an organism with exceptional protein production capabilities modelling of T. reesei can provide novel insight also to other less productive organisms.

Original languageEnglish
Article number132
Pages (from-to)1-26
JournalBiotechnology for Biofuels
Issue number1
Publication statusPublished - 28 Jun 2016
MoE publication typeA1 Journal article-refereed


  • Flux balance analysis
  • Hypocrea jecorina
  • Metabolic modelling
  • Protein production
  • RNA sequencing
  • Stoichiometric model
  • Transcriptomics
  • Trichoderma reesei


Dive into the research topics of 'Genome wide analysis of protein production load in Trichoderma reesei'. Together they form a unique fingerprint.

Cite this