Correlation of gene expression and protein production rate: A system wide study

Mikko Arvas (Corresponding author), Tiina Pakula, Bart Smit, Jari Rautio, Paula Jouhten, Heini Koivistoinen, Erno Lindfors, Marilyn Wiebe, Merja Penttilä, Markku Saloheimo

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

Abstract

The filamentous fungi Trichoderma reesei is an industrial protein production host with exceptional protein secretion capability. It can produce up 100 g/l of protein and it is often used to produce cellulases and hemicellulases to depolymerise biomass. Most efficient production of secreted protein is achieved at low specific growth rate of 0.03 1/h (Pakula et al. Microbiology 151 (2005), 135-143). We have used transcriptomics and proteomics to study the effect of growth rate and cell density to T. reesei protein production in chemostat cultivations. Use of chemostat allows control of growth rate and precise estimation of the specific protein production rate (SPPR). For each gene we calculate its correlation to the SPPR and analyse the distribution of these correlations in context of genome structure and annotation, gene sequence homology to other fungi and predicted metabolic network. Although highest protein production occurs at low growth rate and carbon limitation the observed response is distinct from Saccharomyces cerevisiae's response to low growth rate or carbon limitation. In addition to conventional transcriptomics by microarray, the used microarray also included probes for non-coding sequence to detect novel genes (Arvas et al. Gene 467 (2010) 41-51). Several novel genes, putatively related to regulation, were discovered as differentially expressed in these conditions.
Original languageEnglish
Title of host publication26th Fungal Genetics Conference at Asilomar March 15-20, 2011
PublisherGenetics Society of America
ChapterAbstracts for Posters
Pages120
Publication statusPublished - 2011
MoE publication typeNot Eligible
Event26th Fungal Genetics Conference - Asilomar, United States
Duration: 15 Mar 201120 Mar 2011

Publication series

SeriesFungal Genetics Reports
NumberSupplement
Volume58

Conference

Conference26th Fungal Genetics Conference
CountryUnited States
CityAsilomar
Period15/03/1120/03/11

Fingerprint

gene expression
proteins
Trichoderma reesei
transcriptomics
genes
fungi
protein secretion
cellulases
carbon
microbiology
sequence homology
specific growth rate
proteomics
Saccharomyces cerevisiae
nucleotide sequences
genome
biomass
cells

Cite this

Arvas, M., Pakula, T., Smit, B., Rautio, J., Jouhten, P., Koivistoinen, H., ... Saloheimo, M. (2011). Correlation of gene expression and protein production rate: A system wide study. In 26th Fungal Genetics Conference at Asilomar March 15-20, 2011 (pp. 120). Genetics Society of America. Fungal Genetics Reports, No. Supplement, Vol.. 58
Arvas, Mikko ; Pakula, Tiina ; Smit, Bart ; Rautio, Jari ; Jouhten, Paula ; Koivistoinen, Heini ; Lindfors, Erno ; Wiebe, Marilyn ; Penttilä, Merja ; Saloheimo, Markku. / Correlation of gene expression and protein production rate : A system wide study. 26th Fungal Genetics Conference at Asilomar March 15-20, 2011. Genetics Society of America, 2011. pp. 120 (Fungal Genetics Reports; No. Supplement, Vol. 58).
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abstract = "The filamentous fungi Trichoderma reesei is an industrial protein production host with exceptional protein secretion capability. It can produce up 100 g/l of protein and it is often used to produce cellulases and hemicellulases to depolymerise biomass. Most efficient production of secreted protein is achieved at low specific growth rate of 0.03 1/h (Pakula et al. Microbiology 151 (2005), 135-143). We have used transcriptomics and proteomics to study the effect of growth rate and cell density to T. reesei protein production in chemostat cultivations. Use of chemostat allows control of growth rate and precise estimation of the specific protein production rate (SPPR). For each gene we calculate its correlation to the SPPR and analyse the distribution of these correlations in context of genome structure and annotation, gene sequence homology to other fungi and predicted metabolic network. Although highest protein production occurs at low growth rate and carbon limitation the observed response is distinct from Saccharomyces cerevisiae's response to low growth rate or carbon limitation. In addition to conventional transcriptomics by microarray, the used microarray also included probes for non-coding sequence to detect novel genes (Arvas et al. Gene 467 (2010) 41-51). Several novel genes, putatively related to regulation, were discovered as differentially expressed in these conditions.",
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Arvas, M, Pakula, T, Smit, B, Rautio, J, Jouhten, P, Koivistoinen, H, Lindfors, E, Wiebe, M, Penttilä, M & Saloheimo, M 2011, Correlation of gene expression and protein production rate: A system wide study. in 26th Fungal Genetics Conference at Asilomar March 15-20, 2011. Genetics Society of America, Fungal Genetics Reports, no. Supplement, vol. 58, pp. 120, 26th Fungal Genetics Conference, Asilomar, United States, 15/03/11.

Correlation of gene expression and protein production rate : A system wide study. / Arvas, Mikko (Corresponding author); Pakula, Tiina; Smit, Bart; Rautio, Jari; Jouhten, Paula; Koivistoinen, Heini; Lindfors, Erno; Wiebe, Marilyn; Penttilä, Merja; Saloheimo, Markku.

26th Fungal Genetics Conference at Asilomar March 15-20, 2011. Genetics Society of America, 2011. p. 120 (Fungal Genetics Reports; No. Supplement, Vol. 58).

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

TY - CHAP

T1 - Correlation of gene expression and protein production rate

T2 - A system wide study

AU - Arvas, Mikko

AU - Pakula, Tiina

AU - Smit, Bart

AU - Rautio, Jari

AU - Jouhten, Paula

AU - Koivistoinen, Heini

AU - Lindfors, Erno

AU - Wiebe, Marilyn

AU - Penttilä, Merja

AU - Saloheimo, Markku

N1 - Abstract for poster CA2: TK402 CA2: TK400 CA2: TK401

PY - 2011

Y1 - 2011

N2 - The filamentous fungi Trichoderma reesei is an industrial protein production host with exceptional protein secretion capability. It can produce up 100 g/l of protein and it is often used to produce cellulases and hemicellulases to depolymerise biomass. Most efficient production of secreted protein is achieved at low specific growth rate of 0.03 1/h (Pakula et al. Microbiology 151 (2005), 135-143). We have used transcriptomics and proteomics to study the effect of growth rate and cell density to T. reesei protein production in chemostat cultivations. Use of chemostat allows control of growth rate and precise estimation of the specific protein production rate (SPPR). For each gene we calculate its correlation to the SPPR and analyse the distribution of these correlations in context of genome structure and annotation, gene sequence homology to other fungi and predicted metabolic network. Although highest protein production occurs at low growth rate and carbon limitation the observed response is distinct from Saccharomyces cerevisiae's response to low growth rate or carbon limitation. In addition to conventional transcriptomics by microarray, the used microarray also included probes for non-coding sequence to detect novel genes (Arvas et al. Gene 467 (2010) 41-51). Several novel genes, putatively related to regulation, were discovered as differentially expressed in these conditions.

AB - The filamentous fungi Trichoderma reesei is an industrial protein production host with exceptional protein secretion capability. It can produce up 100 g/l of protein and it is often used to produce cellulases and hemicellulases to depolymerise biomass. Most efficient production of secreted protein is achieved at low specific growth rate of 0.03 1/h (Pakula et al. Microbiology 151 (2005), 135-143). We have used transcriptomics and proteomics to study the effect of growth rate and cell density to T. reesei protein production in chemostat cultivations. Use of chemostat allows control of growth rate and precise estimation of the specific protein production rate (SPPR). For each gene we calculate its correlation to the SPPR and analyse the distribution of these correlations in context of genome structure and annotation, gene sequence homology to other fungi and predicted metabolic network. Although highest protein production occurs at low growth rate and carbon limitation the observed response is distinct from Saccharomyces cerevisiae's response to low growth rate or carbon limitation. In addition to conventional transcriptomics by microarray, the used microarray also included probes for non-coding sequence to detect novel genes (Arvas et al. Gene 467 (2010) 41-51). Several novel genes, putatively related to regulation, were discovered as differentially expressed in these conditions.

M3 - Conference abstract in proceedings

T3 - Fungal Genetics Reports

SP - 120

BT - 26th Fungal Genetics Conference at Asilomar March 15-20, 2011

PB - Genetics Society of America

ER -

Arvas M, Pakula T, Smit B, Rautio J, Jouhten P, Koivistoinen H et al. Correlation of gene expression and protein production rate: A system wide study. In 26th Fungal Genetics Conference at Asilomar March 15-20, 2011. Genetics Society of America. 2011. p. 120. (Fungal Genetics Reports; No. Supplement, Vol. 58).