The effects of extracellular pH and of the transcriptional regulator PACI on the transcriptome of Trichoderma reesei

Mari Häkkinen, Dhinakaran Sivasiddarthan, Nina Aro, Markku Saloheimo, Tiina M. Pakula (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

20 Citations (Scopus)

Abstract

Background: Extracellular pH is one of the several environmental factors affecting protein production by filamentous fungi. Regulatory mechanisms ensure that extracellular enzymes are produced under pH-conditions in which the enzymes are active. In filamentous fungi, the transcriptional regulation in different ambient pH has been studied especially in Aspergilli, whereas the effects of pH in the industrial producer of hydrolytic enzymes, Trichoderma reesei, have mainly been studied at the protein level. In this study, the pH-dependent expression of T. reesei genes was investigated by genome-wide transcriptional profiling and by analysing the effects of deletion of the gene encoding the transcriptional regulator pac1, the orthologue of Aspergillus nidulans pacC gene. Results: Transcriptional analysis revealed the pH-responsive genes of T. reesei, and functional classification of the genes identified the activities most affected by changing pH. A large number of genes encoding especially transporters, signalling-related proteins, extracellular enzymes and proteins involved in different metabolism-related functions were found to be pH-responsive. Several cellulase- and hemicellulase-encoding genes were found among the pH-responsive genes. Especially, genes encoding hemicellulases with the similar type of activity were shown to include both genes up-regulated at low pH and genes up-regulated at high pH. However, relatively few of the cellulase- and hemicellulase-encoding genes showed direct PACI-mediated regulation, indicating the importance of other regulatory mechanisms affecting expression in different pH conditions. New information was gained on the effects of pH on the genes involved in ambient pH-signalling and on the known and candidate regulatory genes involved in regulation of cellulase and hemicellulase encoding genes. In addition, co-regulated genomic clusters responding to change of ambient pH were identified. Conclusions: Ambient pH was shown to be an important determinant of T. reesei gene expression. The pH-responsive genes, including those affected by the regulator of ambient pH sensing, were identified, and novel information on the activity of genes encoding carbohydrate active enzymes at different pH was gained.
Original languageEnglish
Article number63
JournalMicrobial Cell Factories
Volume14
DOIs
Publication statusPublished - 2015
MoE publication typeA1 Journal article-refereed

Fingerprint

Trichoderma
Transcriptome
Gene encoding
Genes
Enzymes
Cellulase
Proteins
Aspergillus
Fungi
Carbohydrates
Metabolism
Gene expression
Aspergillus nidulans

Keywords

  • ambient pH
  • carbohydrate active enzymes
  • cellulase
  • gene expression
  • gene regulation
  • hemicellulase
  • pac 1
  • transcriptional profiling
  • Trichoderma reesei

Cite this

@article{e2660f95e58745e987c0e3cbc8f7cf37,
title = "The effects of extracellular pH and of the transcriptional regulator PACI on the transcriptome of Trichoderma reesei",
abstract = "Background: Extracellular pH is one of the several environmental factors affecting protein production by filamentous fungi. Regulatory mechanisms ensure that extracellular enzymes are produced under pH-conditions in which the enzymes are active. In filamentous fungi, the transcriptional regulation in different ambient pH has been studied especially in Aspergilli, whereas the effects of pH in the industrial producer of hydrolytic enzymes, Trichoderma reesei, have mainly been studied at the protein level. In this study, the pH-dependent expression of T. reesei genes was investigated by genome-wide transcriptional profiling and by analysing the effects of deletion of the gene encoding the transcriptional regulator pac1, the orthologue of Aspergillus nidulans pacC gene. Results: Transcriptional analysis revealed the pH-responsive genes of T. reesei, and functional classification of the genes identified the activities most affected by changing pH. A large number of genes encoding especially transporters, signalling-related proteins, extracellular enzymes and proteins involved in different metabolism-related functions were found to be pH-responsive. Several cellulase- and hemicellulase-encoding genes were found among the pH-responsive genes. Especially, genes encoding hemicellulases with the similar type of activity were shown to include both genes up-regulated at low pH and genes up-regulated at high pH. However, relatively few of the cellulase- and hemicellulase-encoding genes showed direct PACI-mediated regulation, indicating the importance of other regulatory mechanisms affecting expression in different pH conditions. New information was gained on the effects of pH on the genes involved in ambient pH-signalling and on the known and candidate regulatory genes involved in regulation of cellulase and hemicellulase encoding genes. In addition, co-regulated genomic clusters responding to change of ambient pH were identified. Conclusions: Ambient pH was shown to be an important determinant of T. reesei gene expression. The pH-responsive genes, including those affected by the regulator of ambient pH sensing, were identified, and novel information on the activity of genes encoding carbohydrate active enzymes at different pH was gained.",
keywords = "ambient pH, carbohydrate active enzymes, cellulase, gene expression, gene regulation, hemicellulase, pac 1, transcriptional profiling, Trichoderma reesei",
author = "Mari H{\"a}kkinen and Dhinakaran Sivasiddarthan and Nina Aro and Markku Saloheimo and Pakula, {Tiina M.}",
year = "2015",
doi = "10.1186/s12934-015-0247-z",
language = "English",
volume = "14",
journal = "Microbial Cell Factories",
issn = "1475-2859",

}

The effects of extracellular pH and of the transcriptional regulator PACI on the transcriptome of Trichoderma reesei. / Häkkinen, Mari; Sivasiddarthan, Dhinakaran; Aro, Nina; Saloheimo, Markku; Pakula, Tiina M. (Corresponding Author).

In: Microbial Cell Factories, Vol. 14, 63, 2015.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - The effects of extracellular pH and of the transcriptional regulator PACI on the transcriptome of Trichoderma reesei

AU - Häkkinen, Mari

AU - Sivasiddarthan, Dhinakaran

AU - Aro, Nina

AU - Saloheimo, Markku

AU - Pakula, Tiina M.

PY - 2015

Y1 - 2015

N2 - Background: Extracellular pH is one of the several environmental factors affecting protein production by filamentous fungi. Regulatory mechanisms ensure that extracellular enzymes are produced under pH-conditions in which the enzymes are active. In filamentous fungi, the transcriptional regulation in different ambient pH has been studied especially in Aspergilli, whereas the effects of pH in the industrial producer of hydrolytic enzymes, Trichoderma reesei, have mainly been studied at the protein level. In this study, the pH-dependent expression of T. reesei genes was investigated by genome-wide transcriptional profiling and by analysing the effects of deletion of the gene encoding the transcriptional regulator pac1, the orthologue of Aspergillus nidulans pacC gene. Results: Transcriptional analysis revealed the pH-responsive genes of T. reesei, and functional classification of the genes identified the activities most affected by changing pH. A large number of genes encoding especially transporters, signalling-related proteins, extracellular enzymes and proteins involved in different metabolism-related functions were found to be pH-responsive. Several cellulase- and hemicellulase-encoding genes were found among the pH-responsive genes. Especially, genes encoding hemicellulases with the similar type of activity were shown to include both genes up-regulated at low pH and genes up-regulated at high pH. However, relatively few of the cellulase- and hemicellulase-encoding genes showed direct PACI-mediated regulation, indicating the importance of other regulatory mechanisms affecting expression in different pH conditions. New information was gained on the effects of pH on the genes involved in ambient pH-signalling and on the known and candidate regulatory genes involved in regulation of cellulase and hemicellulase encoding genes. In addition, co-regulated genomic clusters responding to change of ambient pH were identified. Conclusions: Ambient pH was shown to be an important determinant of T. reesei gene expression. The pH-responsive genes, including those affected by the regulator of ambient pH sensing, were identified, and novel information on the activity of genes encoding carbohydrate active enzymes at different pH was gained.

AB - Background: Extracellular pH is one of the several environmental factors affecting protein production by filamentous fungi. Regulatory mechanisms ensure that extracellular enzymes are produced under pH-conditions in which the enzymes are active. In filamentous fungi, the transcriptional regulation in different ambient pH has been studied especially in Aspergilli, whereas the effects of pH in the industrial producer of hydrolytic enzymes, Trichoderma reesei, have mainly been studied at the protein level. In this study, the pH-dependent expression of T. reesei genes was investigated by genome-wide transcriptional profiling and by analysing the effects of deletion of the gene encoding the transcriptional regulator pac1, the orthologue of Aspergillus nidulans pacC gene. Results: Transcriptional analysis revealed the pH-responsive genes of T. reesei, and functional classification of the genes identified the activities most affected by changing pH. A large number of genes encoding especially transporters, signalling-related proteins, extracellular enzymes and proteins involved in different metabolism-related functions were found to be pH-responsive. Several cellulase- and hemicellulase-encoding genes were found among the pH-responsive genes. Especially, genes encoding hemicellulases with the similar type of activity were shown to include both genes up-regulated at low pH and genes up-regulated at high pH. However, relatively few of the cellulase- and hemicellulase-encoding genes showed direct PACI-mediated regulation, indicating the importance of other regulatory mechanisms affecting expression in different pH conditions. New information was gained on the effects of pH on the genes involved in ambient pH-signalling and on the known and candidate regulatory genes involved in regulation of cellulase and hemicellulase encoding genes. In addition, co-regulated genomic clusters responding to change of ambient pH were identified. Conclusions: Ambient pH was shown to be an important determinant of T. reesei gene expression. The pH-responsive genes, including those affected by the regulator of ambient pH sensing, were identified, and novel information on the activity of genes encoding carbohydrate active enzymes at different pH was gained.

KW - ambient pH

KW - carbohydrate active enzymes

KW - cellulase

KW - gene expression

KW - gene regulation

KW - hemicellulase

KW - pac 1

KW - transcriptional profiling

KW - Trichoderma reesei

U2 - 10.1186/s12934-015-0247-z

DO - 10.1186/s12934-015-0247-z

M3 - Article

VL - 14

JO - Microbial Cell Factories

JF - Microbial Cell Factories

SN - 1475-2859

M1 - 63

ER -