Genome wide analysis of protein production load in Trichoderma reesei

Research output: Contribution to journalArticleScientificpeer-review

8 Citations (Scopus)

Abstract

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
Number of pages26
JournalBiotechnology for Biofuels
Volume9
DOIs
Publication statusPublished - 2016
MoE publication typeA1 Journal article-refereed

Fingerprint

Trichoderma
genome
Genes
Genome
Proteins
protein
Metabolism
metabolism
Cellulases
modeling
analysis
Hypocrea
RNA Sequence Analysis
Secretory Pathway
Bioreactors
Protein Transport
Physiology
Transcriptome
Sulfur
Glycerol

Keywords

  • flux balance analysis
  • hypocrea jecorina
  • metabolic modelling
  • protein production
  • RNA sequencing
  • stoichiometric model
  • transcriptomics
  • trichoderma reesei

Cite this

@article{fc0de28b068342d2bd60acd88f0f81b0,
title = "Genome wide analysis of protein production load in Trichoderma reesei",
abstract = "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.",
keywords = "flux balance analysis, hypocrea jecorina, metabolic modelling, protein production, RNA sequencing, stoichiometric model, transcriptomics, trichoderma reesei",
author = "Tiina Pakula and Heli Nygr{\'e}n and Dorothee Barth and Markus Heinonen and Castillo, {Sandra D.} and Penttil{\"a}, {Merja E.} and Mikko Arvas",
year = "2016",
doi = "10.1186/s13068-016-0547-5",
language = "English",
volume = "9",
journal = "Biotechnology for Biofuels",
issn = "1754-6834",

}

Genome wide analysis of protein production load in Trichoderma reesei. / Pakula, Tiina; Nygrén, Heli; Barth, Dorothee; Heinonen, Markus; Castillo, Sandra D.; Penttilä, Merja E.; Arvas, Mikko.

In: Biotechnology for Biofuels, Vol. 9, 2016.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Genome wide analysis of protein production load in Trichoderma reesei

AU - Pakula, Tiina

AU - Nygrén, Heli

AU - Barth, Dorothee

AU - Heinonen, Markus

AU - Castillo, Sandra D.

AU - Penttilä, Merja E.

AU - Arvas, Mikko

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - flux balance analysis

KW - hypocrea jecorina

KW - metabolic modelling

KW - protein production

KW - RNA sequencing

KW - stoichiometric model

KW - transcriptomics

KW - trichoderma reesei

U2 - 10.1186/s13068-016-0547-5

DO - 10.1186/s13068-016-0547-5

M3 - Article

VL - 9

JO - Biotechnology for Biofuels

JF - Biotechnology for Biofuels

SN - 1754-6834

ER -