Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis

Jari J. Rautio (Corresponding Author), Michael Bailey, Teemu Kivioja, Hans Söderlund, Merja Penttilä, Markku Saloheimo

Research output: Contribution to journalArticleScientificpeer-review

8 Citations (Scopus)

Abstract

Background: Biologically relevant molecular markers can be used in evaluation of the physiological state of an organism in biotechnical processes. We monitored at high frequency the expression of 34 marker genes in batch, fed-batch and continuous cultures of the filamentous fungus Trichoderma reesei by the transcriptional analysis method TRAC (TRanscript analysis with the aid of Affinity Capture). Expression of specific genes was normalised either with respect to biomass or to overall polyA RNA concentration. Expressional variation of the genes involved in various process relevant cellular functions, such as protein production, growth and stress responses, was related to process parameters such as specific growth and production rates and substrate and dissolved oxygen concentrations. Results: Gene expression of secreted cellulases and recombinant Melanocarpus albomyces laccase predicted the trends in the corresponding extracellular enzyme production rates and was highest in a narrow "physiological window" in the specific growth rate (μ) range of 0.03 - 0.05 h-1. Expression of ribosomal protein mRNAs was consistent with the changes in μ. Nine starvation-related genes were found as potential markers for detection of insufficient substrate feed for maintaining optimal protein production. For two genes induced in anaerobic conditions, increasing transcript levels were measured as dissolved oxygen decreased. Conclusion: The data obtained by TRAC supported the usefulness of focused and intensive transcriptional analysis in monitoring of biotechnical processes providing thus tools for process optimisation purposes.

Original languageEnglish
Article number28
Number of pages16
JournalBMC Biotechnology
Volume7
DOIs
Publication statusPublished - 30 May 2007
MoE publication typeA1 Journal article-refereed

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Trichoderma
Fungi
Gene Expression
Genes
Growth
Oxygen
Cellulases
Laccase
Batch Cell Culture Techniques
Ribosomal Proteins
Starvation
Biomass
Proteins
RNA
Messenger RNA
Enzymes

Cite this

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title = "Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis",
abstract = "Background: Biologically relevant molecular markers can be used in evaluation of the physiological state of an organism in biotechnical processes. We monitored at high frequency the expression of 34 marker genes in batch, fed-batch and continuous cultures of the filamentous fungus Trichoderma reesei by the transcriptional analysis method TRAC (TRanscript analysis with the aid of Affinity Capture). Expression of specific genes was normalised either with respect to biomass or to overall polyA RNA concentration. Expressional variation of the genes involved in various process relevant cellular functions, such as protein production, growth and stress responses, was related to process parameters such as specific growth and production rates and substrate and dissolved oxygen concentrations. Results: Gene expression of secreted cellulases and recombinant Melanocarpus albomyces laccase predicted the trends in the corresponding extracellular enzyme production rates and was highest in a narrow {"}physiological window{"} in the specific growth rate (μ) range of 0.03 - 0.05 h-1. Expression of ribosomal protein mRNAs was consistent with the changes in μ. Nine starvation-related genes were found as potential markers for detection of insufficient substrate feed for maintaining optimal protein production. For two genes induced in anaerobic conditions, increasing transcript levels were measured as dissolved oxygen decreased. Conclusion: The data obtained by TRAC supported the usefulness of focused and intensive transcriptional analysis in monitoring of biotechnical processes providing thus tools for process optimisation purposes.",
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Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis. / Rautio, Jari J. (Corresponding Author); Bailey, Michael; Kivioja, Teemu; Söderlund, Hans; Penttilä, Merja; Saloheimo, Markku.

In: BMC Biotechnology, Vol. 7, 28, 30.05.2007.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis

AU - Rautio, Jari J.

AU - Bailey, Michael

AU - Kivioja, Teemu

AU - Söderlund, Hans

AU - Penttilä, Merja

AU - Saloheimo, Markku

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AB - Background: Biologically relevant molecular markers can be used in evaluation of the physiological state of an organism in biotechnical processes. We monitored at high frequency the expression of 34 marker genes in batch, fed-batch and continuous cultures of the filamentous fungus Trichoderma reesei by the transcriptional analysis method TRAC (TRanscript analysis with the aid of Affinity Capture). Expression of specific genes was normalised either with respect to biomass or to overall polyA RNA concentration. Expressional variation of the genes involved in various process relevant cellular functions, such as protein production, growth and stress responses, was related to process parameters such as specific growth and production rates and substrate and dissolved oxygen concentrations. Results: Gene expression of secreted cellulases and recombinant Melanocarpus albomyces laccase predicted the trends in the corresponding extracellular enzyme production rates and was highest in a narrow "physiological window" in the specific growth rate (μ) range of 0.03 - 0.05 h-1. Expression of ribosomal protein mRNAs was consistent with the changes in μ. Nine starvation-related genes were found as potential markers for detection of insufficient substrate feed for maintaining optimal protein production. For two genes induced in anaerobic conditions, increasing transcript levels were measured as dissolved oxygen decreased. Conclusion: The data obtained by TRAC supported the usefulness of focused and intensive transcriptional analysis in monitoring of biotechnical processes providing thus tools for process optimisation purposes.

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