Rapid gene expression analysis for evaluation of physiological state of micro-organisms

Jari Rautio, Mervi Toivari, Bart Smit, Michael Bailey, Hans Söderlund, Markku Saloheimo, Merja Penttilä

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

Abstract

Micro-organisms used in various types of biotechnical processes encounter constantly changing environmental conditions, to which they adapt by changing their cellular physiology. The performance of the used micro-organism has a major impact on the performance of the biotechnical process, and as a consequence, bioprocess monitoring and control strategies based on the physiological status of the cells culture have become more popular. Transcriptional analysis of selected marker genes is a potential way for robust monitoring of physiological events. However, tools suitable for high-throughput expression monitoring of process-relevant genes are scarce. We have applied a novel transcriptional analysis method called TRAC (TRanscript analysis with aid of Affinity Capture) for frequent expression analysis of a focused gene set in a wide range of fungal fermentations. TRAC method allows fast expression analysis of dozens of mRNAs from crude cell lysates by solution hybridisation with a pool of target-specific oligonucleotide probes of distinct sizes that are identified and quantified by capillary electrophoresis. The assay procedure has been semi-automated for simultaneous treatment of 96 samples using a magnetic bead particle processor. The whole assay procedure can be performed in few hours, implying its usefulness in bioprocess monitoring and control. We have used TRAC for instance to monitor the physiological state of the filamentous fungus Trichoderma during protein production processes and S. cerevisiae physiology in various chemostat cultures and brewing processes. By process relevant gene markers it is possible to evaluate the growth and extracellular protein production potential of the culture as well as physiological responses to various stress conditions such as lack of nutrients and oxygen or limitation of the protein folding capacity. TRAC also provides a quick and affordable means to monitor transient situations, and to address the quality and stability of e.g. chemostat cultures prior to selecting samples for more thorough and expensive systems-wide analyses.
Original languageEnglish
Title of host publicationInternational Specialised Symposium on Yeasts ISSY25
Subtitle of host publicationSystems Biology of Yeasts - from Models to Applications
Place of PublicationEspoo
PublisherVTT Technical Research Centre of Finland
Pages58
ISBN (Electronic)951-38-6308-5
ISBN (Print)951-38-6307-7
Publication statusPublished - 2006
EventInternational Specialised Symposium on Yeasts, ISSY 25 - Espoo, Finland
Duration: 18 Jun 200621 Jun 2006

Publication series

SeriesVTT Symposium
Number242
ISSN0357-9387

Conference

ConferenceInternational Specialised Symposium on Yeasts, ISSY 25
Abbreviated titleISSY 25
CountryFinland
CityEspoo
Period18/06/0621/06/06

Fingerprint

physiological state
microorganisms
gene expression
monitoring
physiology
process monitoring
genetic markers
oligonucleotide probes
protein folding
capillary electrophoresis
brewing
Trichoderma
assays
plant response
stress response
cell culture
hybridization
genes
proteins
fermentation

Cite this

Rautio, J., Toivari, M., Smit, B., Bailey, M., Söderlund, H., Saloheimo, M., & Penttilä, M. (2006). Rapid gene expression analysis for evaluation of physiological state of micro-organisms. In International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications (pp. 58). [P6] Espoo: VTT Technical Research Centre of Finland. VTT Symposium, No. 242
Rautio, Jari ; Toivari, Mervi ; Smit, Bart ; Bailey, Michael ; Söderlund, Hans ; Saloheimo, Markku ; Penttilä, Merja. / Rapid gene expression analysis for evaluation of physiological state of micro-organisms. International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo : VTT Technical Research Centre of Finland, 2006. pp. 58 (VTT Symposium; No. 242).
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Rautio, J, Toivari, M, Smit, B, Bailey, M, Söderlund, H, Saloheimo, M & Penttilä, M 2006, Rapid gene expression analysis for evaluation of physiological state of micro-organisms. in International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications., P6, VTT Technical Research Centre of Finland, Espoo, VTT Symposium, no. 242, pp. 58, International Specialised Symposium on Yeasts, ISSY 25 , Espoo, Finland, 18/06/06.

Rapid gene expression analysis for evaluation of physiological state of micro-organisms. / Rautio, Jari; Toivari, Mervi; Smit, Bart; Bailey, Michael; Söderlund, Hans; Saloheimo, Markku; Penttilä, Merja.

International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo : VTT Technical Research Centre of Finland, 2006. p. 58 P6 (VTT Symposium; No. 242).

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

TY - CHAP

T1 - Rapid gene expression analysis for evaluation of physiological state of micro-organisms

AU - Rautio, Jari

AU - Toivari, Mervi

AU - Smit, Bart

AU - Bailey, Michael

AU - Söderlund, Hans

AU - Saloheimo, Markku

AU - Penttilä, Merja

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N2 - Micro-organisms used in various types of biotechnical processes encounter constantly changing environmental conditions, to which they adapt by changing their cellular physiology. The performance of the used micro-organism has a major impact on the performance of the biotechnical process, and as a consequence, bioprocess monitoring and control strategies based on the physiological status of the cells culture have become more popular. Transcriptional analysis of selected marker genes is a potential way for robust monitoring of physiological events. However, tools suitable for high-throughput expression monitoring of process-relevant genes are scarce. We have applied a novel transcriptional analysis method called TRAC (TRanscript analysis with aid of Affinity Capture) for frequent expression analysis of a focused gene set in a wide range of fungal fermentations. TRAC method allows fast expression analysis of dozens of mRNAs from crude cell lysates by solution hybridisation with a pool of target-specific oligonucleotide probes of distinct sizes that are identified and quantified by capillary electrophoresis. The assay procedure has been semi-automated for simultaneous treatment of 96 samples using a magnetic bead particle processor. The whole assay procedure can be performed in few hours, implying its usefulness in bioprocess monitoring and control. We have used TRAC for instance to monitor the physiological state of the filamentous fungus Trichoderma during protein production processes and S. cerevisiae physiology in various chemostat cultures and brewing processes. By process relevant gene markers it is possible to evaluate the growth and extracellular protein production potential of the culture as well as physiological responses to various stress conditions such as lack of nutrients and oxygen or limitation of the protein folding capacity. TRAC also provides a quick and affordable means to monitor transient situations, and to address the quality and stability of e.g. chemostat cultures prior to selecting samples for more thorough and expensive systems-wide analyses.

AB - Micro-organisms used in various types of biotechnical processes encounter constantly changing environmental conditions, to which they adapt by changing their cellular physiology. The performance of the used micro-organism has a major impact on the performance of the biotechnical process, and as a consequence, bioprocess monitoring and control strategies based on the physiological status of the cells culture have become more popular. Transcriptional analysis of selected marker genes is a potential way for robust monitoring of physiological events. However, tools suitable for high-throughput expression monitoring of process-relevant genes are scarce. We have applied a novel transcriptional analysis method called TRAC (TRanscript analysis with aid of Affinity Capture) for frequent expression analysis of a focused gene set in a wide range of fungal fermentations. TRAC method allows fast expression analysis of dozens of mRNAs from crude cell lysates by solution hybridisation with a pool of target-specific oligonucleotide probes of distinct sizes that are identified and quantified by capillary electrophoresis. The assay procedure has been semi-automated for simultaneous treatment of 96 samples using a magnetic bead particle processor. The whole assay procedure can be performed in few hours, implying its usefulness in bioprocess monitoring and control. We have used TRAC for instance to monitor the physiological state of the filamentous fungus Trichoderma during protein production processes and S. cerevisiae physiology in various chemostat cultures and brewing processes. By process relevant gene markers it is possible to evaluate the growth and extracellular protein production potential of the culture as well as physiological responses to various stress conditions such as lack of nutrients and oxygen or limitation of the protein folding capacity. TRAC also provides a quick and affordable means to monitor transient situations, and to address the quality and stability of e.g. chemostat cultures prior to selecting samples for more thorough and expensive systems-wide analyses.

M3 - Conference abstract in proceedings

SN - 951-38-6307-7

T3 - VTT Symposium

SP - 58

BT - International Specialised Symposium on Yeasts ISSY25

PB - VTT Technical Research Centre of Finland

CY - Espoo

ER -

Rautio J, Toivari M, Smit B, Bailey M, Söderlund H, Saloheimo M et al. Rapid gene expression analysis for evaluation of physiological state of micro-organisms. In International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo: VTT Technical Research Centre of Finland. 2006. p. 58. P6. (VTT Symposium; No. 242).