List of works - Merja Penttilä

13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose

scientific article

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

scientific article

A novel NADH-linked l-xylulose reductase in the l-arabinose catabolic pathway of yeast

scientific article

A novel aldose-aldose oxidoreductase for co-production of D-xylonate and xylitol from D-xylose with Saccharomyces cerevisiae

scientific article published on 12 August 2015

A novel two-step extraction method with detergent/polymer systems for primary recovery of the fusion protein endoglucanase I-hydrophobin I.

scientific article published in January 2002

ACEI of Trichoderma reesei is a repressor of cellulase and xylanase expression

scientific article

Activation mechanisms of the HAC1-mediated unfolded protein response in filamentous fungi

scientific article

Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties

scientific article

Assigning probes into a small number of pools separable by electrophoresis

scientific article published in January 2002

Atomic resolution structure of the HFBII hydrophobin, a self-assembling amphiphile

scientific article

Bioconversion of D-galacturonate to keto-deoxy-L-galactonate (3-deoxy-L-threo-hex-2-ulosonate) using filamentous fungi

scientific article

Capillary electrophoresis for the monitoring of carboxylic acid production by Gluconobacter oxydans

scientific article published on 4 January 2010

Capillary electrophoresis for the monitoring of phenolic compounds in bioprocesses

scholarly article by Heidi Turkia et al published February 2013 in Journal of Chromatography

Capillary electrophoresis with laser-induced fluorescence detection for studying amino acid uptake by yeast during beer fermentation

scientific article

Categorisation of sugar acid dehydratases in Aspergillus niger

scientific article

Central carbon metabolism of Saccharomyces cerevisiae in anaerobic, oxygen-limited and fully aerobic steady-state conditions and following a shift to anaerobic conditions

scientific article published on 10 April 2007

Characterisation of two 14-3-3 genes from Trichoderma reesei: interactions with yeast secretory pathway components

scientific article

Characterization of secretory genes ypt1/yptA and nsf1/nsfA from two filamentous fungi: induction of secretory pathway genes of Trichoderma reesei under secretion stress conditions

scientific article published on January 2004

Characterization of the Ashbya gossypii secreted N-glycome and genomic insights into its N-glycosylation pathway

scientific article

Cloning and characterization of the glucosidase II alpha subunit gene of Trichoderma reesei: a frameshift mutation results in the aberrant glycosylation profile of the hypercellulolytic strain Rut-C30

scientific article published on June 2005

Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae

scientific article

Correlation of gene expression and protein production rate - a system wide study

scientific article

Detecting novel genes with sparse arrays

scientific article

Direct identification of hydrophobins and their processing in Trichoderma using intact-cell MALDI-TOF MS.

scientific article

Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis

scientific article

Effects of inactivation and constitutive expression of the unfolded- protein response pathway on protein production in the yeast Saccharomyces cerevisiae

scientific article

Efficient production of L-lactic acid from xylose by Pichia stipitis

scientific article published on 27 October 2006

Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei

scientific article published on 26 August 2015

Endogenous xylose pathway in Saccharomyces cerevisiae

scientific article published on June 2004

Engineering chimeric thermostable GH7 cellobiohydrolases in Saccharomyces cerevisiae

scientific article published on 23 August 2013

Engineering filamentous fungi for conversion of D-galacturonic acid to L-galactonic acid

scientific article published on 5 October 2012

Engineering redox cofactor regeneration for improved pentose fermentation in Saccharomyces cerevisiae

scientific article

Enhanced Triacylglycerol Production With Genetically Modified Trichosporon oleaginosus.

scientific article

Enhancing the flux of D-glucose to the pentose phosphate pathway in Saccharomyces cerevisiae for the production of D-ribose and ribitol

scientific article published on 27 August 2009

Enzymatic properties and intracellular localization of the novel Trichoderma reesei beta-glucosidase BGLII (cel1A)

scientific article

Expression in Trichoderma reesei and characterisation of a thermostable family 3 beta-glucosidase from the moderately thermophilic fungus Talaromyces emersonii

scientific article published in December 2004

Extraction of endoglucanase I (Cel7B) fusion proteins from Trichoderma reesei culture filtrate in a poly(ethylene glycol)–phosphate aqueous two-phase system

article

Genetic modification of carbon catabolite repression in Trichoderma reesei for improved protein production

scientific article published on 15 May 2009

Genome wide analysis of protein production load in Trichoderma reesei

scientific article published on 28 June 2016

Glycolic acid production in the engineered yeasts Saccharomyces cerevisiae and Kluyveromyces lactis

scientific article (publication date: 23 September 2013)

High level secretion of cellobiohydrolases by Saccharomyces cerevisiae

scientific article

High speed atomic force microscopy visualizes processive movement of Trichoderma reesei cellobiohydrolase I on crystalline cellulose

scientific article

Identification in Agrobacterium tumefaciens of the D-galacturonic acid dehydrogenase gene

scientific article

Identification in the mold Hypocrea jecorina of the first fungal D-galacturonic acid reductase

scientific article published in August 2005

Identification in the yeast Pichia stipitis of the first L-rhamnose-1-dehydrogenase gene

scientific article published on 8 April 2008

Identification of an L-arabinose reductase gene in Aspergillus niger and its role in L-arabinose catabolism

scientific article published on 28 May 2010

Improvement of foreign-protein production in Aspergillus niger var. awamori by constitutive induction of the unfolded-protein response

scientific article published on December 2003

Influence of growth temperature on the production of antibody Fab fragments in different microbes: a host comparative analysis.

scientific article published on 23 December 2010

Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae

scientific article

Investigation of protein secretion and secretion stress in Ashbya gossypii

scientific article

L-arabinose/D-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of L-arabinose to L-arabonate with Saccharomyces cerevisiae

scientific article published on 19 September 2014

L-lactic acid production from D-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene

scientific article published on 8 August 2014

Lipid production in batch and fed-batch cultures of Rhodosporidium toruloides from 5 and 6 carbon carbohydrates

scientific article

Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae

scientific article

Low pH D-xylonate production with Pichia kudriavzevii

scientific article published on 7 February 2013

Metabolic engineering of Saccharomyces cerevisiae for conversion of D-glucose to xylitol and other five-carbon sugars and sugar alcohols

scientific article published on 13 July 2007

Metabolic engineering of fungal strains for conversion of D-galacturonate to meso-galactarate

scientific article published on 6 November 2009

Metabolic engineering of the fungal D-galacturonate pathway for L-ascorbic acid production

scientific article published on 8 January 2015

Metabolic flux analysis of xylose metabolism in recombinant Saccharomyces cerevisiae using continuous culture

scientific article published in January 2003

Microbial D-xylonate production

scientific article

Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions

scientific article

Noninvasive high-throughput single-cell analysis of the intracellular pH of Saccharomyces cerevisiae by ratiometric flow cytometry

scientific article published on 13 September 2013

Nutritional requirements and strain heterogeneity in Ashbya gossypii

scientific article published on 5 December 2011

Online capillary electrophoresis for monitoring carboxylic acid production by yeast during bioreactor cultivations

scientific article published on 4 October 2013

Optimization of cDNA-AFLP experiments using genomic sequence data

scientific article

Overexpression of PAD1 and FDC1 results in significant cinnamic acid decarboxylase activity in Saccharomyces cerevisiae

scientific article

Overexpression of an endochitinase gene (ThEn-42) in Trichoderma atroviride for increased production of antifungal enzymes and enhanced antagonist action against pathogenic fungi

scientific article

Overexpression of the gene encoding GTP:mannose-1-phosphate guanyltransferase, mpg1, increases cellular GDP-mannose levels and protein mannosylation in Trichoderma reesei

scientific article

Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A.

scientific article

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

scientific article

Primary recovery of a genetically engineered Trichoderma reesei endoglucanase I (Cel 7B) fusion protein in cloud point extraction systems

scientific article

Production and applications of carbohydrate-derived sugar acids as generic biobased chemicals

scientific article published on 15 July 2015

Production of L-lactic acid by the yeast Candida sonorensis expressing heterologous bacterial and fungal lactate dehydrogenases

scientific article (publication date: 25 May 2013)

Production of ethanol from L-arabinose by Saccharomyces cerevisiae containing a fungal L-arabinose pathway

scientific article published in April 2003

Production of ethylene glycol or glycolic acid from D-xylose in Saccharomyces cerevisiae

scientific article

Protein production and induction of the unfolded protein response in Trichoderma reesei strain Rut-C30 and its transformant expressing endoglucanase I with a hydrophobic tag.

scientific article published in February 2005

Proteome analysis of recombinant xylose-fermenting Saccharomyces cerevisiae

scientific article

Purification, crystallization and preliminary X-ray diffraction analysis of the Trichoderma reesei hydrophobin HFBI.

scientific article published on 23 September 2004

Random and direct mutagenesis to enhance protein secretion in Ashbya gossypii

scientific article published on 15 April 2013

Rapid and multiplexed transcript analysis of microbial cultures using capillary electophoresis-detectable oligonucleotide probe pools

scientific article published on 29 September 2005

Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates ⬇️

scientific article published on October 4, 2012

Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae

scientific article published on 4 June 2008

Role of Ace2 (Activator of Cellulases 2) within the xyn2 transcriptosome of Hypocrea jecorina

scientific article published on 28 August 2007

Saccharomyces cerevisiae engineered to produce D-xylonate

scientific article published on 3 August 2010

Screening of candidate regulators for cellulase and hemicellulase production in Trichoderma reesei and identification of a factor essential for cellulase production

scientific article published on 28 January 2014

Single-cell measurements of enzyme levels as a predictive tool for cellular fates during organic acid production

scientific article (publication date: December 2013)

Spatially segregated SNARE protein interactions in living fungal cells

scientific article published on 5 June 2007

Surface adhesion of fusion proteins containing the hydrophobins HFBI and HFBII from Trichoderma reesei

scientific article published on September 2002

Swollenin aids in the amorphogenesis step during the enzymatic hydrolysis of pretreated biomass

scientific article published on 23 May 2013

Swollenin, a Trichoderma reesei protein with sequence similarity to the plant expansins, exhibits disruption activity on cellulosic materials

scientific article

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae

scientific article

The 'true' L-xylulose reductase of filamentous fungi identified in Aspergillus niger

scientific article published on 21 July 2010

The ORF YNL274c (GOR1) codes for glyoxylate reductase in Saccharomyces cerevisiae

scientific article

The diverse role of Pdr12 in resistance to weak organic acids.

scientific article

The effect of specific growth rate on protein synthesis and secretion in the filamentous fungus Trichoderma reesei

scientific article published in January 2005

The effects of disruption of phosphoglucose isomerase gene on carbon utilisation and cellulase production in Trichoderma reesei Rut-C30 ⬇️

scientific article published on May 24, 2011

The effects of drugs inhibiting protein secretion in the filamentous fungus Trichoderma reesei. Evidence for down-regulation of genes that encode secreted proteins in the stressed cells

scientific article published on 26 August 2003

The missing link in the fungal D-galacturonate pathway: identification of the L-threo-3-deoxy-hexulosonate aldolase

scientific article published on 3 July 2007

The missing link in the fungal L-arabinose catabolic pathway, identification of the L-xylulose reductase gene

scientific article

The use of carbohydrate binding modules (CBMs) to monitor changes in fragmentation and cellulose fiber surface morphology during cellulase- and Swollenin-induced deconstruction of lignocellulosic substrates

scientific article

Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili

scholarly article by Michael Lienemann et al published 17 September 2018 in Microbial Biotechnology

Transcription analysis of recombinant saccharomyces cerevisiae reveals novel responses to xylose

scientific article

Transcription of hexose transporters of Saccharomyces cerevisiae is affected by change in oxygen provision

scientific article

Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei

scientific article

Transcriptional regulation of plant cell wall degradation by filamentous fungi

scientific article

Transcriptional regulation of xyn1, encoding xylanase I, in Hypocrea jecorina

scientific article published on March 2006

Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism

scientific article

Transcriptome of Saccharomyces cerevisiae during production of D-xylonate

scientific article

Xylanase XYN IV from Trichoderma reesei showing exo- and endo-xylanase activity

scientific article published on 20 December 2012

Xylose chemostat isolates of Saccharomyces cerevisiae show altered metabolite and enzyme levels compared with xylose, glucose, and ethanol metabolism of the original strain

scientific article published on 4 January 2005

Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures

scientific article published on 10 October 2015

Yeast as a tool to express sugar acid transporters with biotechnological interest

scientific article published on 12 January 2017

Yeast oligo-mediated genome engineering (YOGE).

scientific article

List of works by Merja Penttilä

13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

A novel NADH-linked l-xylulose reductase in the l-arabinose catabolic pathway of yeast

A novel aldose-aldose oxidoreductase for co-production of D-xylonate and xylitol from D-xylose with Saccharomyces cerevisiae

A novel two-step extraction method with detergent/polymer systems for primary recovery of the fusion protein endoglucanase I-hydrophobin I.

ACEI of Trichoderma reesei is a repressor of cellulase and xylanase expression

Activation mechanisms of the HAC1-mediated unfolded protein response in filamentous fungi

Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties

Assigning probes into a small number of pools separable by electrophoresis

Atomic resolution structure of the HFBII hydrophobin, a self-assembling amphiphile

Bioconversion of D-galacturonate to keto-deoxy-L-galactonate (3-deoxy-L-threo-hex-2-ulosonate) using filamentous fungi

Capillary electrophoresis for the monitoring of carboxylic acid production by Gluconobacter oxydans

Capillary electrophoresis for the monitoring of phenolic compounds in bioprocesses

Capillary electrophoresis with laser-induced fluorescence detection for studying amino acid uptake by yeast during beer fermentation

Categorisation of sugar acid dehydratases in Aspergillus niger

Central carbon metabolism of Saccharomyces cerevisiae in anaerobic, oxygen-limited and fully aerobic steady-state conditions and following a shift to anaerobic conditions

Characterisation of two 14-3-3 genes from Trichoderma reesei: interactions with yeast secretory pathway components

Characterization of secretory genes ypt1/yptA and nsf1/nsfA from two filamentous fungi: induction of secretory pathway genes of Trichoderma reesei under secretion stress conditions

Characterization of the Ashbya gossypii secreted N-glycome and genomic insights into its N-glycosylation pathway

Cloning and characterization of the glucosidase II alpha subunit gene of Trichoderma reesei: a frameshift mutation results in the aberrant glycosylation profile of the hypercellulolytic strain Rut-C30

Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae

Correlation of gene expression and protein production rate - a system wide study

Detecting novel genes with sparse arrays

Direct identification of hydrophobins and their processing in Trichoderma using intact-cell MALDI-TOF MS.

Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis

Effects of inactivation and constitutive expression of the unfolded- protein response pathway on protein production in the yeast Saccharomyces cerevisiae

Efficient production of L-lactic acid from xylose by Pichia stipitis

Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei

Endogenous xylose pathway in Saccharomyces cerevisiae

Engineering chimeric thermostable GH7 cellobiohydrolases in Saccharomyces cerevisiae

Engineering filamentous fungi for conversion of D-galacturonic acid to L-galactonic acid

Engineering redox cofactor regeneration for improved pentose fermentation in Saccharomyces cerevisiae

Enhanced Triacylglycerol Production With Genetically Modified Trichosporon oleaginosus.

Enhancing the flux of D-glucose to the pentose phosphate pathway in Saccharomyces cerevisiae for the production of D-ribose and ribitol

Enzymatic properties and intracellular localization of the novel Trichoderma reesei beta-glucosidase BGLII (cel1A)

Expression in Trichoderma reesei and characterisation of a thermostable family 3 beta-glucosidase from the moderately thermophilic fungus Talaromyces emersonii

Extraction of endoglucanase I (Cel7B) fusion proteins from Trichoderma reesei culture filtrate in a poly(ethylene glycol)–phosphate aqueous two-phase system

Genetic modification of carbon catabolite repression in Trichoderma reesei for improved protein production

Genome wide analysis of protein production load in Trichoderma reesei

Glycolic acid production in the engineered yeasts Saccharomyces cerevisiae and Kluyveromyces lactis

High level secretion of cellobiohydrolases by Saccharomyces cerevisiae

High speed atomic force microscopy visualizes processive movement of Trichoderma reesei cellobiohydrolase I on crystalline cellulose

Identification in Agrobacterium tumefaciens of the D-galacturonic acid dehydrogenase gene

Identification in the mold Hypocrea jecorina of the first fungal D-galacturonic acid reductase

Identification in the yeast Pichia stipitis of the first L-rhamnose-1-dehydrogenase gene

Identification of an L-arabinose reductase gene in Aspergillus niger and its role in L-arabinose catabolism

Improvement of foreign-protein production in Aspergillus niger var. awamori by constitutive induction of the unfolded-protein response

Influence of growth temperature on the production of antibody Fab fragments in different microbes: a host comparative analysis.

Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae

Investigation of protein secretion and secretion stress in Ashbya gossypii

L-arabinose/D-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of L-arabinose to L-arabonate with Saccharomyces cerevisiae

L-lactic acid production from D-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene

Lipid production in batch and fed-batch cultures of Rhodosporidium toruloides from 5 and 6 carbon carbohydrates

Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae

Low pH D-xylonate production with Pichia kudriavzevii

Metabolic engineering of Saccharomyces cerevisiae for conversion of D-glucose to xylitol and other five-carbon sugars and sugar alcohols

Metabolic engineering of fungal strains for conversion of D-galacturonate to meso-galactarate

Metabolic engineering of the fungal D-galacturonate pathway for L-ascorbic acid production

Metabolic flux analysis of xylose metabolism in recombinant Saccharomyces cerevisiae using continuous culture

Microbial D-xylonate production

Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions

Noninvasive high-throughput single-cell analysis of the intracellular pH of Saccharomyces cerevisiae by ratiometric flow cytometry

Nutritional requirements and strain heterogeneity in Ashbya gossypii

Online capillary electrophoresis for monitoring carboxylic acid production by yeast during bioreactor cultivations

Optimization of cDNA-AFLP experiments using genomic sequence data

Overexpression of PAD1 and FDC1 results in significant cinnamic acid decarboxylase activity in Saccharomyces cerevisiae

Overexpression of an endochitinase gene (ThEn-42) in Trichoderma atroviride for increased production of antifungal enzymes and enhanced antagonist action against pathogenic fungi

Overexpression of the gene encoding GTP:mannose-1-phosphate guanyltransferase, mpg1, increases cellular GDP-mannose levels and protein mannosylation in Trichoderma reesei

Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A.

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

Primary recovery of a genetically engineered Trichoderma reesei endoglucanase I (Cel 7B) fusion protein in cloud point extraction systems

Production and applications of carbohydrate-derived sugar acids as generic biobased chemicals

Production of L-lactic acid by the yeast Candida sonorensis expressing heterologous bacterial and fungal lactate dehydrogenases

Production of ethanol from L-arabinose by Saccharomyces cerevisiae containing a fungal L-arabinose pathway

Production of ethylene glycol or glycolic acid from D-xylose in Saccharomyces cerevisiae

Protein production and induction of the unfolded protein response in Trichoderma reesei strain Rut-C30 and its transformant expressing endoglucanase I with a hydrophobic tag.

Proteome analysis of recombinant xylose-fermenting Saccharomyces cerevisiae

Purification, crystallization and preliminary X-ray diffraction analysis of the Trichoderma reesei hydrophobin HFBI.

Random and direct mutagenesis to enhance protein secretion in Ashbya gossypii